1     M         1.451   1.451   1.451   1.602   1.602   1.602   1.451   1.451   1.451
2     G        -0.685  -0.685  -0.685  -0.561  -0.561  -0.561  -0.685  -0.685  -0.685
3     V        -0.685  -0.685  -0.685  -0.818  -0.818  -0.818  -0.685  -0.685  -0.685
4     Y        -0.685  -0.685  -0.685  -0.520  -0.520  -0.520  -0.685  -0.685  -0.685
5     L        -0.685  -0.685  -0.685  -0.848  -0.848  -0.848  -0.685  -0.685  -0.685
6     A        -0.685  -0.685  -0.685  -0.603  -0.603  -0.603  -0.685  -0.685  -0.685
7     V        -0.685  -0.685  -0.685  -0.999  -0.999  -0.999  -0.685  -0.685  -0.685
8     L        -0.685  -0.685  -0.685  -0.999  -0.999  -0.999  -0.685  -0.685  -0.685
9     F         1.451   1.451   1.451   1.545   1.545   1.545   1.451   1.451   1.451
10    S        -0.685  -0.685  -0.685  -0.561  -0.561  -0.561  -0.685  -0.685  -0.685
11    L        -0.685  -0.685  -0.685  -0.908  -0.908  -0.908  -0.685  -0.685  -0.685
12    L         1.451   1.451   1.451   0.989   0.989   0.989   1.451   1.451   1.451
13    V        -0.685  -0.685  -0.685  -0.818  -0.818  -0.818  -0.685  -0.685  -0.685
14    I        -0.685  -0.685  -0.685  -1.139  -1.139  -1.139  -0.685  -0.685  -0.685
15    E         1.451   1.451   1.451   1.545   1.545   1.545   1.451   1.451   1.451
16    M         1.451   1.451   1.451   1.602   1.602   1.602   1.451   1.451   1.451
17    A        -0.685  -0.685  -0.685  -0.603  -0.603  -0.603  -0.685  -0.685  -0.685
18    I        -0.685  -0.685  -0.685  -0.659  -0.659  -0.659  -0.685  -0.685  -0.685
19    L         1.451   1.451   1.451   0.989   0.989   0.989   1.451   1.451   1.451
20    F        -0.685  -0.685  -0.685  -0.893  -0.893  -0.893  -0.685  -0.685  -0.685
21    I        -0.685  -0.685  -0.685  -1.139  -1.139  -1.139  -0.685  -0.685  -0.685
22    L        -0.685  -0.685  -0.685  -0.848  -0.848  -0.848  -0.685  -0.685  -0.685
23    V         1.451   1.451   1.451   1.410   1.410   1.410   1.451   1.451   1.451
24    L         1.451   1.451   1.451   0.989   0.989   0.989   1.451   1.451   1.451
25    P         1.451   1.451   1.451   1.714   1.714   1.714   1.451   1.451   1.451
26    L         1.451   1.451   1.451   0.989   0.989   0.989   1.451   1.451   1.451
27    P         1.451   1.451   1.451   1.714   1.714   1.714   1.451   1.451   1.451
28    Q        -0.685  -0.685  -0.685  -0.278  -0.278  -0.278  -0.685  -0.685  -0.685
29    R        -0.685  -0.685  -0.685  -0.397  -0.397  -0.397  -0.685  -0.685  -0.685
30    M        -0.685  -0.685  -0.685  -0.547  -0.547  -0.547  -0.685  -0.685  -0.685
31    R         1.451   1.451   1.451   1.507   1.507   1.507   1.451   1.451   1.451
32    R        -0.685  -0.685  -0.685  -0.617  -0.617  -0.617  -0.685  -0.685  -0.685
33    W        -0.685  -0.685  -0.685  -0.478  -0.478  -0.478  -0.685  -0.685  -0.685
34    L        -0.685  -0.685  -0.685  -1.139  -1.139  -1.139  -0.685  -0.685  -0.685
35    Y        -0.685  -0.685  -0.685  -0.465  -0.465  -0.465  -0.685  -0.685  -0.685
36    I        -0.685  -0.685  -0.685  -0.645  -0.645  -0.645  -0.685  -0.685  -0.685
37    R        -0.685  -0.685  -0.685  -0.745  -0.745  -0.745  -0.685  -0.685  -0.685
38    Y        -0.685  -0.685  -0.685  -0.520  -0.520  -0.520  -0.685  -0.685  -0.685
39    S        -0.685  -0.685  -0.685  -0.533  -0.533  -0.533  -0.685  -0.685  -0.685
40    I        -0.685  -0.685  -0.685  -0.818  -0.818  -0.818  -0.685  -0.685  -0.685
41    I        -0.685  -0.685  -0.685  -1.139  -1.139  -1.139  -0.685  -0.685  -0.685
42    S        -0.685  -0.685  -0.685  -0.617  -0.617  -0.617  -0.685  -0.685  -0.685
43    T        -0.685  -0.685  -0.685  -0.397  -0.397  -0.397  -0.685  -0.685  -0.685
44    N        -0.685  -0.685  -0.685  -0.848  -0.848  -0.848  -0.685  -0.685  -0.685
45    K         1.451   1.451   1.451   1.293   1.293   1.293   1.451   1.451   1.451
46    K        -0.685  -0.685  -0.685  -0.631  -0.631  -0.631  -0.685  -0.685  -0.685
47    F         1.451   1.451   1.451   1.545   1.545   1.545   1.451   1.451   1.451
48    R        -0.685  -0.685  -0.685  -0.702  -0.702  -0.702  -0.685  -0.685  -0.685
49    T        -0.685  -0.685  -0.685  -0.659  -0.659  -0.659  -0.685  -0.685  -0.685
50    Y        -0.685  -0.685  -0.685  -0.478  -0.478  -0.478  -0.685  -0.685  -0.685
51    M        -0.685  -0.685  -0.685  -0.451  -0.451  -0.451  -0.685  -0.685  -0.685
52    V        -0.685  -0.685  -0.685  -0.397  -0.397  -0.397  -0.685  -0.685  -0.685
53    G        -0.685  -0.685  -0.685  -0.465  -0.465  -0.465  -0.685  -0.685  -0.685
54    I        -0.685  -0.685  -0.685  -0.659  -0.659  -0.659  -0.685  -0.685  -0.685
55    M        -0.685  -0.685  -0.685  -0.547  -0.547  -0.547  -0.685  -0.685  -0.685
56    I         1.451   1.451   1.451   1.233   1.233   1.233   1.451   1.451   1.451
57    F        -0.685  -0.685  -0.685  -0.893  -0.893  -0.893  -0.685  -0.685  -0.685
58    V        -0.685  -0.685  -0.685  -0.999  -0.999  -0.999  -0.685  -0.685  -0.685
59    G        -0.685  -0.685  -0.685  -0.561  -0.561  -0.561  -0.685  -0.685  -0.685
60    L        -0.685  -0.685  -0.685  -0.848  -0.848  -0.848  -0.685  -0.685  -0.685
61    L        -0.685  -0.685  -0.685  -0.908  -0.908  -0.908  -0.685  -0.685  -0.685
62    F         1.451   1.451   1.451   1.545   1.545   1.545   1.451   1.451   1.451
63    I        -0.685  -0.685  -0.685  -0.731  -0.731  -0.731  -0.685  -0.685  -0.685
64    D         1.451   1.451   1.451   1.639   1.639   1.639   1.451   1.451   1.451
65    S        -0.685  -0.685  -0.685  -0.371  -0.371  -0.371  -0.685  -0.685  -0.685
66    W        -0.685  -0.685  -0.685  -0.520  -0.520  -0.520  -0.685  -0.685  -0.685
67    K        -0.685  -0.685  -0.685  -0.688  -0.688  -0.688  -0.685  -0.685  -0.685
68    R         1.451   1.451   1.451   1.507   1.507   1.507   1.451   1.451   1.451
69    S        -0.685  -0.685  -0.685  -0.999  -0.999  -0.999  -0.685  -0.685  -0.685
70    Q         1.451   1.451   1.451   1.526   1.526   1.526   1.451   1.451   1.451
71    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    V        -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    T        -0.685  -0.685  -0.685  -0.465  -0.465  -0.465  -0.685  -0.685  -0.685
76    Y        -0.685  -0.685  -0.685  -0.506  -0.506  -0.506  -0.685  -0.685  -0.685
77    R        -0.685  -0.685  -0.685  -0.492  -0.492  -0.492  -0.685  -0.685  -0.685
78    N        -0.685  -0.685  -0.685  -0.397  -0.397  -0.397  -0.685  -0.685  -0.685
79    Q        -0.685  -0.685  -0.685  -0.908  -0.908  -0.908  -0.685  -0.685  -0.685
80    K        -0.685  -0.685  -0.685  -0.645  -0.645  -0.645  -0.685  -0.685  -0.685
81    N         1.451   1.451   1.451   1.602   1.602   1.602   1.451   1.451   1.451
82    P         1.451   1.451   1.451   1.714   1.714   1.714   1.451   1.451   1.451
83    Y         1.451   1.451   1.451   1.526   1.526   1.526   1.451   1.451   1.451
84    I        -0.685  -0.685  -0.685  -0.717  -0.717  -0.717  -0.685  -0.685  -0.685
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    I        -0.685  -0.685  -0.685  -1.139  -1.139  -1.139  -0.685  -0.685  -0.685
87    N         1.451   1.451   1.451   1.602   1.602   1.602   1.451   1.451   1.451
88    S         1.451   1.451   1.451   1.410   1.410   1.410   1.451   1.451   1.451
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    V        -0.685  -0.685  -0.685  -0.533  -0.533  -0.533  -0.685  -0.685  -0.685
96    T        -0.685  -0.685  -0.685  -0.397  -0.397  -0.397  -0.685  -0.685  -0.685
97    P        -0.685  -0.685  -0.685  -0.465  -0.465  -0.465  -0.685  -0.685  -0.685
98    V        -0.685  -0.685  -0.685  -0.603  -0.603  -0.603  -0.685  -0.685  -0.685
99    D         1.451   1.451   1.451   1.639   1.639   1.639   1.451   1.451   1.451
100   A        -0.685  -0.685  -0.685  -0.520  -0.520  -0.520  -0.685  -0.685  -0.685
101   L         1.451   1.451   1.451   0.989   0.989   0.989   1.451   1.451   1.451
102   A         1.451   1.451   1.451   1.526   1.526   1.526   1.451   1.451   1.451
103   S         1.451   1.451   1.451   1.410   1.410   1.410   1.451   1.451   1.451
104   R        -0.685  -0.685  -0.685  -0.702  -0.702  -0.702  -0.685  -0.685  -0.685
105   A        -0.685  -0.685  -0.685  -0.506  -0.506  -0.506  -0.685  -0.685  -0.685
106   Y         1.451   1.451   1.451   1.526   1.526   1.526   1.451   1.451   1.451
107   N        -0.685  -0.685  -0.685  -0.547  -0.547  -0.547  -0.685  -0.685  -0.685
108   Q         1.451   1.451   1.451   1.526   1.526   1.526   1.451   1.451   1.451
109   R         1.451   1.451   1.451   1.507   1.507   1.507   1.451   1.451   1.451
110   N         1.451   1.451   1.451   1.602   1.602   1.602   1.451   1.451   1.451
111   V        -0.685  -0.685  -0.685  -0.999  -0.999  -0.999  -0.685  -0.685  -0.685
112   Y         1.451   1.451   1.451   1.526   1.526   1.526   1.451   1.451   1.451
113   I         1.451   1.451   1.451   1.233   1.233   1.233   1.451   1.451   1.451
114   S        -0.685  -0.685  -0.685  -0.533  -0.533  -0.533  -0.685  -0.685  -0.685
115   G         1.451   1.451   1.451   1.583   1.583   1.583   1.451   1.451   1.451
116   F        -0.685  -0.685  -0.685  -0.506  -0.506  -0.506  -0.685  -0.685  -0.685
117   I        -0.685  -0.685  -0.685  -0.818  -0.818  -0.818  -0.685  -0.685  -0.685
118   I        -0.685  -0.685  -0.685  -1.139  -1.139  -1.139  -0.685  -0.685  -0.685
119   Y         1.451   1.451   1.451   1.526   1.526   1.526   1.451   1.451   1.451
120   F        -0.685  -0.685  -0.685  -0.893  -0.893  -0.893  -0.685  -0.685  -0.685
121   Y        -0.685  -0.685  -0.685  -0.465  -0.465  -0.465  -0.685  -0.685  -0.685
122   I        -0.685  -0.685  -0.685  -1.139  -1.139  -1.139  -0.685  -0.685  -0.685
123   C        -0.685  -0.685  -0.685  -0.291  -0.291  -0.291  -0.685  -0.685  -0.685
124   I         1.451   1.451   1.451   1.233   1.233   1.233   1.451   1.451   1.451
125   L        -0.685  -0.685  -0.685  -0.908  -0.908  -0.908  -0.685  -0.685  -0.685
126   T         1.451   1.451   1.451   1.621   1.621   1.621   1.451   1.451   1.451
127   V         1.451   1.451   1.451   1.410   1.410   1.410   1.451   1.451   1.451
128   M        -0.685  -0.685  -0.685  -0.547  -0.547  -0.547  -0.685  -0.685  -0.685
129   S        -0.685  -0.685  -0.685  -0.533  -0.533  -0.533  -0.685  -0.685  -0.685
130   I         1.451   1.451   1.451   1.233   1.233   1.233   1.451   1.451   1.451
131   L         1.451   1.451   1.451   0.989   0.989   0.989   1.451   1.451   1.451
132   R        -0.685  -0.685  -0.685  -0.702  -0.702  -0.702  -0.685  -0.685  -0.685
133   R        -0.685  -0.685  -0.685  -0.702  -0.702  -0.702  -0.685  -0.685  -0.685
134   I        -0.685  -0.685  -0.685  -1.139  -1.139  -1.139  -0.685  -0.685  -0.685
135   V         1.451   1.451   1.451   1.410   1.410   1.410   1.451   1.451   1.451
136   E        -0.685  -0.685  -0.685  -0.589  -0.589  -0.589  -0.685  -0.685  -0.685
137   W        -0.685  -0.685  -0.685  -0.478  -0.478  -0.478  -0.685  -0.685  -0.685
138   N        -0.685  -0.685  -0.685  -0.451  -0.451  -0.451  -0.685  -0.685  -0.685
139   D        -0.685  -0.685  -0.685  -0.438  -0.438  -0.438  -0.685  -0.685  -0.685
140   K        -0.685  -0.685  -0.685  -0.674  -0.674  -0.674  -0.685  -0.685  -0.685
141   M        -0.685  -0.685  -0.685  -0.451  -0.451  -0.451  -0.685  -0.685  -0.685
142   K        -0.685  -0.685  -0.685  -0.702  -0.702  -0.702  -0.685  -0.685  -0.685
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
153   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
154   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   A         1.451   1.451   1.451   1.526   1.526   1.526   1.451   1.451   1.451
157   G         1.451   1.451   1.451   1.583   1.583   1.583   1.451   1.451   1.451
158   D        -0.685  -0.685  -0.685  -0.424  -0.424  -0.424  -0.685  -0.685  -0.685
159   D        -0.685  -0.685  -0.685  -0.424  -0.424  -0.424  -0.685  -0.685  -0.685
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
167   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
171   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
176   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   I        -0.685  -0.685  -0.685  -0.659  -0.659  -0.659  -0.685  -0.685  -0.685
183   L         1.451   1.451   1.451   0.989   0.989   0.989   1.451   1.451   1.451
184   K         1.451   1.451   1.451   1.293   1.293   1.293   1.451   1.451   1.451
185   E        -0.685  -0.685  -0.685  -0.674  -0.674  -0.674  -0.685  -0.685  -0.685
186   K        -0.685  -0.685  -0.685  -0.688  -0.688  -0.688  -0.685  -0.685  -0.685
187   L        -0.685  -0.685  -0.685  -0.999  -0.999  -0.999  -0.685  -0.685  -0.685
188   R        -0.685  -0.685  -0.685  -0.492  -0.492  -0.492  -0.685  -0.685  -0.685
189   R        -0.685  -0.685  -0.685  -0.492  -0.492  -0.492  -0.685  -0.685  -0.685
190   K        -0.685  -0.685  -0.685  -1.092  -1.092  -1.092  -0.685  -0.685  -0.685
191   Q         1.451   1.451   1.451   1.526   1.526   1.526   1.451   1.451   1.451
192   K         1.451   1.451   1.451   1.293   1.293   1.293   1.451   1.451   1.451
193   Y        -0.685  -0.685  -0.685  -0.603  -0.603  -0.603  -0.685  -0.685  -0.685
194   L        -0.685  -0.685  -0.685  -0.908  -0.908  -0.908  -0.685  -0.685  -0.685
195   E        -0.685  -0.685  -0.685  -0.424  -0.424  -0.424  -0.685  -0.685  -0.685
196   E        -0.685  -0.685  -0.685  -0.424  -0.424  -0.424  -0.685  -0.685  -0.685
197   L         1.451   1.451   1.451   0.989   0.989   0.989   1.451   1.451   1.451
198   Q        -0.685  -0.685  -0.685  -0.465  -0.465  -0.465  -0.685  -0.685  -0.685
199   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
201   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
202   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
203   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
204   K        -0.685  -0.685  -0.685  -0.603  -0.603  -0.603  -0.685  -0.685  -0.685
205   K         1.451   1.451   1.451   1.293   1.293   1.293   1.451   1.451   1.451
206   K        -0.685  -0.685  -0.685  -0.603  -0.603  -0.603  -0.685  -0.685  -0.685
207   F        -0.685  -0.685  -0.685  -0.492  -0.492  -0.492  -0.685  -0.685  -0.685
* 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/Q04210
Output conservation file - output/Q04210
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
