1     M         1.284   1.284   1.284   1.512   1.512   1.512   1.284   1.284   1.284
2     S         1.284   1.284   1.284   1.048   1.048   1.048   1.284   1.284   1.284
3     A        -0.773  -0.773  -0.773  -0.353  -0.353  -0.353  -0.773  -0.773  -0.773
4     N        -0.773  -0.773  -0.773  -1.133  -1.133  -1.133  -0.773  -0.773  -0.773
5     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     G         1.284   1.284   1.284   1.312   1.312   1.312   1.284   1.284   1.284
10    K        -0.773  -0.773  -0.773  -1.181  -1.181  -1.181  -0.773  -0.773  -0.773
11    L         1.284   1.284   1.284   1.440   1.440   1.440   1.284   1.284   1.284
12    S         1.284   1.284   1.284   1.048   1.048   1.048   1.284   1.284   1.284
13    S         1.284   1.284   1.284   1.048   1.048   1.048   1.284   1.284   1.284
14    R         1.284   1.284   1.284   1.368   1.368   1.368   1.284   1.284   1.284
15    V         1.284   1.284   1.284   1.422   1.422   1.422   1.284   1.284   1.284
16    M         1.284   1.284   1.284   1.512   1.512   1.512   1.284   1.284   1.284
17    N         1.284   1.284   1.284   1.220   1.220   1.220   1.284   1.284   1.284
18    M         1.284   1.284   1.284   1.512   1.512   1.512   1.284   1.284   1.284
19    K         1.284   1.284   1.284   0.564   0.564   0.564   1.284   1.284   1.284
20    F         1.284   1.284   1.284   1.512   1.512   1.512   1.284   1.284   1.284
21    M         1.284   1.284   1.284   1.512   1.512   1.512   1.284   1.284   1.284
22    K         1.284   1.284   1.284   0.564   0.564   0.564   1.284   1.284   1.284
23    F         1.284   1.284   1.284   1.512   1.512   1.512   1.284   1.284   1.284
24    G        -0.773  -0.773  -0.773  -0.366  -0.366  -0.366  -0.773  -0.773  -0.773
25    K        -0.773  -0.773  -0.773  -1.009  -1.009  -1.009  -0.773  -0.773  -0.773
26    T        -0.773  -0.773  -0.773  -0.189  -0.189  -0.189  -0.773  -0.773  -0.773
27    D        -0.773  -0.773  -0.773  -0.730  -0.730  -0.730  -0.773  -0.773  -0.773
28    D        -0.773  -0.773  -0.773  -0.619  -0.619  -0.619  -0.773  -0.773  -0.773
29    E        -0.773  -0.773  -0.773  -0.405  -0.405  -0.405  -0.773  -0.773  -0.773
30    E        -0.773  -0.773  -0.773  -0.730  -0.730  -0.730  -0.773  -0.773  -0.773
31    S        -0.773  -0.773  -0.773  -0.773  -0.773  -0.773  -0.773  -0.773  -0.773
32    S        -0.773  -0.773  -0.773  -1.278  -1.278  -1.278  -0.773  -0.773  -0.773
33    N        -0.773  -0.773  -0.773  -0.688  -0.688  -0.688  -0.773  -0.773  -0.773
34    S        -0.773  -0.773  -0.773  -0.816  -0.816  -0.816  -0.773  -0.773  -0.773
35    N        -0.773  -0.773  -0.773  -0.578  -0.578  -0.578  -0.773  -0.773  -0.773
36    T         1.284   1.284   1.284   1.494   1.494   1.494   1.284   1.284   1.284
37    P        -0.773  -0.773  -0.773  -0.497  -0.497  -0.497  -0.773  -0.773  -0.773
38    S        -0.773  -0.773  -0.773  -1.278  -1.278  -1.278  -0.773  -0.773  -0.773
39    N        -0.773  -0.773  -0.773  -0.366  -0.366  -0.366  -0.773  -0.773  -0.773
40    I        -0.773  -0.773  -0.773  -0.226  -0.226  -0.226  -0.773  -0.773  -0.773
41    N        -0.773  -0.773  -0.773  -0.366  -0.366  -0.366  -0.773  -0.773  -0.773
42    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    L         1.284   1.284   1.284   1.440   1.440   1.440   1.284   1.284   1.284
57    D         1.284   1.284   1.284   1.163   1.163   1.163   1.284   1.284   1.284
58    D        -0.773  -0.773  -0.773  -0.457  -0.457  -0.457  -0.773  -0.773  -0.773
59    S         1.284   1.284   1.284   1.048   1.048   1.048   1.284   1.284   1.284
60    A        -0.773  -0.773  -0.773  -0.874  -0.874  -0.874  -0.773  -0.773  -0.773
61    W         1.284   1.284   1.284   1.670   1.670   1.670   1.284   1.284   1.284
62    D         1.284   1.284   1.284   1.163   1.163   1.163   1.284   1.284   1.284
63    L         1.284   1.284   1.284   1.440   1.440   1.440   1.284   1.284   1.284
64    N        -0.773  -0.773  -0.773  -1.133  -1.133  -1.133  -0.773  -0.773  -0.773
65    S         1.284   1.284   1.284   1.048   1.048   1.048   1.284   1.284   1.284
66    Y        -0.773  -0.773  -0.773  -0.457  -0.457  -0.457  -0.773  -0.773  -0.773
67    K        -0.773  -0.773  -0.773  -0.963  -0.963  -0.963  -0.773  -0.773  -0.773
68    D        -0.773  -0.773  -0.773  -0.688  -0.688  -0.688  -0.773  -0.773  -0.773
69    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    K        -0.773  -0.773  -0.773  -1.278  -1.278  -1.278  -0.773  -0.773  -0.773
77    E        -0.773  -0.773  -0.773  -0.730  -0.730  -0.730  -0.773  -0.773  -0.773
78    K        -0.773  -0.773  -0.773  -1.278  -1.278  -1.278  -0.773  -0.773  -0.773
79    K        -0.773  -0.773  -0.773  -0.904  -0.904  -0.904  -0.773  -0.773  -0.773
80    K        -0.773  -0.773  -0.773  -1.133  -1.133  -1.133  -0.773  -0.773  -0.773
81    V        -0.773  -0.773  -0.773  -0.963  -0.963  -0.963  -0.773  -0.773  -0.773
82    K        -0.773  -0.773  -0.773  -1.009  -1.009  -1.009  -0.773  -0.773  -0.773
83    R         1.284   1.284   1.284   1.368   1.368   1.368   1.284   1.284   1.284
84    V         1.284   1.284   1.284   1.422   1.422   1.422   1.284   1.284   1.284
85    V         1.284   1.284   1.284   1.422   1.422   1.422   1.284   1.284   1.284
86    Y        -0.773  -0.773  -0.773  -0.201  -0.201  -0.201  -0.773  -0.773  -0.773
87    K         1.284   1.284   1.284   0.564   0.564   0.564   1.284   1.284   1.284
88    K        -0.773  -0.773  -0.773  -1.009  -1.009  -1.009  -0.773  -0.773  -0.773
89    R        -0.773  -0.773  -0.773  -0.314  -0.314  -0.314  -0.773  -0.773  -0.773
90    P        -0.773  -0.773  -0.773  -0.497  -0.497  -0.497  -0.773  -0.773  -0.773
91    N        -0.773  -0.773  -0.773  -1.133  -1.133  -1.133  -0.773  -0.773  -0.773
92    L        -0.773  -0.773  -0.773  -0.264  -0.264  -0.264  -0.773  -0.773  -0.773
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    I         1.284   1.284   1.284   1.530   1.530   1.530   1.284   1.284   1.284
96    I        -0.773  -0.773  -0.773  -0.213  -0.213  -0.213  -0.773  -0.773  -0.773
97    S        -0.773  -0.773  -0.773  -0.816  -0.816  -0.816  -0.773  -0.773  -0.773
98    N         1.284   1.284   1.284   1.220   1.220   1.220   1.284   1.284   1.284
99    V         1.284   1.284   1.284   1.422   1.422   1.422   1.284   1.284   1.284
100   G         1.284   1.284   1.284   1.312   1.312   1.312   1.284   1.284   1.284
101   Y        -0.773  -0.773  -0.773  -0.127  -0.127  -0.127  -0.773  -0.773  -0.773
102   S        -0.773  -0.773  -0.773  -0.564  -0.564  -0.564  -0.773  -0.773  -0.773
103   E        -0.773  -0.773  -0.773  -0.816  -0.816  -0.816  -0.773  -0.773  -0.773
104   L        -0.773  -0.773  -0.773  -0.340  -0.340  -0.340  -0.773  -0.773  -0.773
105   R        -0.773  -0.773  -0.773  -1.009  -1.009  -1.009  -0.773  -0.773  -0.773
106   K        -0.773  -0.773  -0.773  -0.874  -0.874  -0.874  -0.773  -0.773  -0.773
107   P        -0.773  -0.773  -0.773  -0.418  -0.418  -0.418  -0.773  -0.773  -0.773
108   E        -0.773  -0.773  -0.773  -0.730  -0.730  -0.730  -0.773  -0.773  -0.773
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   G        -0.773  -0.773  -0.773  -0.702  -0.702  -0.702  -0.773  -0.773  -0.773
115   V        -0.773  -0.773  -0.773  -0.276  -0.276  -0.276  -0.773  -0.773  -0.773
116   I        -0.773  -0.773  -0.773  -0.264  -0.264  -0.264  -0.773  -0.773  -0.773
117   S        -0.773  -0.773  -0.773  -0.484  -0.484  -0.484  -0.773  -0.773  -0.773
118   G         1.284   1.284   1.284   1.312   1.312   1.312   1.284   1.284   1.284
119   R         1.284   1.284   1.284   1.368   1.368   1.368   1.284   1.284   1.284
120   K        -0.773  -0.773  -0.773  -1.009  -1.009  -1.009  -0.773  -0.773  -0.773
121   T        -0.773  -0.773  -0.773  -0.226  -0.226  -0.226  -0.773  -0.773  -0.773
122   F         1.284   1.284   1.284   1.512   1.512   1.512   1.284   1.284   1.284
123   G         1.284   1.284   1.284   1.312   1.312   1.312   1.284   1.284   1.284
124   D        -0.773  -0.773  -0.773  -0.730  -0.730  -0.730  -0.773  -0.773  -0.773
125   N         1.284   1.284   1.284   1.220   1.220   1.220   1.284   1.284   1.284
126   S        -0.773  -0.773  -0.773  -1.278  -1.278  -1.278  -0.773  -0.773  -0.773
127   D        -0.773  -0.773  -0.773  -0.688  -0.688  -0.688  -0.773  -0.773  -0.773
128   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   K         1.284   1.284   1.284   0.564   0.564   0.564   1.284   1.284   1.284
134   R         1.284   1.284   1.284   1.368   1.368   1.368   1.284   1.284   1.284
135   K        -0.773  -0.773  -0.773  -0.963  -0.963  -0.963  -0.773  -0.773  -0.773
136   F        -0.773  -0.773  -0.773  -0.213  -0.213  -0.213  -0.773  -0.773  -0.773
137   D        -0.773  -0.773  -0.773  -0.730  -0.730  -0.730  -0.773  -0.773  -0.773
138   E         1.284   1.284   1.284   1.163   1.163   1.163   1.284   1.284   1.284
139   G        -0.773  -0.773  -0.773  -0.619  -0.619  -0.619  -0.773  -0.773  -0.773
140   E         1.284   1.284   1.284   1.163   1.163   1.163   1.284   1.284   1.284
141   Q        -0.773  -0.773  -0.773  -0.405  -0.405  -0.405  -0.773  -0.773  -0.773
142   N         1.284   1.284   1.284   1.220   1.220   1.220   1.284   1.284   1.284
143   E        -0.773  -0.773  -0.773  -1.181  -1.181  -1.181  -0.773  -0.773  -0.773
144   D        -0.773  -0.773  -0.773  -0.484  -0.484  -0.484  -0.773  -0.773  -0.773
145   E         1.284   1.284   1.284   1.163   1.163   1.163   1.284   1.284   1.284
146   K        -0.773  -0.773  -0.773  -0.816  -0.816  -0.816  -0.773  -0.773  -0.773
147   R        -0.773  -0.773  -0.773  -0.578  -0.578  -0.578  -0.773  -0.773  -0.773
148   D        -0.773  -0.773  -0.773  -0.418  -0.418  -0.418  -0.773  -0.773  -0.773
149   A        -0.773  -0.773  -0.773  -0.874  -0.874  -0.874  -0.773  -0.773  -0.773
150   K        -0.773  -0.773  -0.773  -0.816  -0.816  -0.816  -0.773  -0.773  -0.773
151   D        -0.773  -0.773  -0.773  -0.730  -0.730  -0.730  -0.773  -0.773  -0.773
152   K         1.284   1.284   1.284   0.564   0.564   0.564   1.284   1.284   1.284
153   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
158   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
159   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
160   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   D         1.284   1.284   1.284   1.163   1.163   1.163   1.284   1.284   1.284
167   L        -0.773  -0.773  -0.773  -0.276  -0.276  -0.276  -0.773  -0.773  -0.773
168   D         1.284   1.284   1.284   1.163   1.163   1.163   1.284   1.284   1.284
169   K        -0.773  -0.773  -0.773  -1.181  -1.181  -1.181  -0.773  -0.773  -0.773
170   L         1.284   1.284   1.284   1.440   1.440   1.440   1.284   1.284   1.284
171   F         1.284   1.284   1.284   1.512   1.512   1.512   1.284   1.284   1.284
172   K         1.284   1.284   1.284   0.564   0.564   0.564   1.284   1.284   1.284
173   D        -0.773  -0.773  -0.773  -0.730  -0.730  -0.730  -0.773  -0.773  -0.773
174   S         1.284   1.284   1.284   1.048   1.048   1.048   1.284   1.284   1.284
175   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   K        -0.773  -0.773  -0.773  -1.009  -1.009  -1.009  -0.773  -0.773  -0.773
178   K        -0.773  -0.773  -0.773  -1.009  -1.009  -1.009  -0.773  -0.773  -0.773
179   K        -0.773  -0.773  -0.773  -1.133  -1.133  -1.133  -0.773  -0.773  -0.773
180   T         1.284   1.284   1.284   1.494   1.494   1.494   1.284   1.284   1.284
181   N        -0.773  -0.773  -0.773  -1.133  -1.133  -1.133  -0.773  -0.773  -0.773
182   H        -0.773  -0.773  -0.773  -0.115  -0.115  -0.115  -0.773  -0.773  -0.773
183   N        -0.773  -0.773  -0.773  -1.133  -1.133  -1.133  -0.773  -0.773  -0.773
184   G        -0.773  -0.773  -0.773  -1.055  -1.055  -1.055  -0.773  -0.773  -0.773
185   K         1.284   1.284   1.284   0.564   0.564   0.564   1.284   1.284   1.284
186   N        -0.773  -0.773  -0.773  -0.773  -0.773  -0.773  -0.773  -0.773  -0.773
187   K        -0.773  -0.773  -0.773  -0.816  -0.816  -0.816  -0.773  -0.773  -0.773
188   N        -0.773  -0.773  -0.773  -1.133  -1.133  -1.133  -0.773  -0.773  -0.773
189   R        -0.773  -0.773  -0.773  -1.009  -1.009  -1.009  -0.773  -0.773  -0.773
190   N        -0.773  -0.773  -0.773  -0.366  -0.366  -0.366  -0.773  -0.773  -0.773
191   S        -0.773  -0.773  -0.773  -1.278  -1.278  -1.278  -0.773  -0.773  -0.773
192   K         1.284   1.284   1.284   0.564   0.564   0.564   1.284   1.284   1.284
193   K        -0.773  -0.773  -0.773  -0.874  -0.874  -0.874  -0.773  -0.773  -0.773
* 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/P53725
Output conservation file - output/P53725
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
