1     M         1.275   1.275   1.275   1.585   1.585   1.585   1.275   1.275   1.275
2     D        -0.779  -0.779  -0.779  -0.577  -0.577  -0.577  -0.779  -0.779  -0.779
3     L        -0.779  -0.779  -0.779  -0.870  -0.870  -0.870  -0.779  -0.779  -0.779
4     K        -0.779  -0.779  -0.779  -0.683  -0.683  -0.683  -0.779  -0.779  -0.779
5     R        -0.779  -0.779  -0.779  -0.967  -0.967  -0.967  -0.779  -0.779  -0.779
6     D        -0.779  -0.779  -0.779  -0.607  -0.607  -0.607  -0.779  -0.779  -0.779
7     W        -0.779  -0.779  -0.779  -0.401  -0.401  -0.401  -0.779  -0.779  -0.779
8     L        -0.779  -0.779  -0.779  -1.033  -1.033  -1.033  -0.779  -0.779  -0.779
9     R         1.275   1.275   1.275   1.358   1.358   1.358   1.275   1.275   1.275
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    W        -0.779  -0.779  -0.779  -0.259  -0.259  -0.259  -0.779  -0.779  -0.779
13    K        -0.779  -0.779  -0.779  -0.791  -0.791  -0.791  -0.779  -0.779  -0.779
14    I         1.275   1.275   1.275   0.924   0.924   0.924   1.275   1.275   1.275
15    T        -0.779  -0.779  -0.779  -0.668  -0.668  -0.668  -0.779  -0.779  -0.779
16    I        -0.779  -0.779  -0.779  -0.919  -0.919  -0.919  -0.779  -0.779  -0.779
17    G        -0.779  -0.779  -0.779  -0.776  -0.776  -0.776  -0.779  -0.779  -0.779
18    S        -0.779  -0.779  -0.779  -0.902  -0.902  -0.902  -0.779  -0.779  -0.779
19    G         1.275   1.275   1.275   1.188   1.188   1.188   1.275   1.275   1.275
20    P        -0.779  -0.779  -0.779  -0.607  -0.607  -0.607  -0.779  -0.779  -0.779
21    G        -0.779  -0.779  -0.779  -0.776  -0.776  -0.776  -0.779  -0.779  -0.779
22    S        -0.779  -0.779  -0.779  -0.729  -0.729  -0.729  -0.779  -0.779  -0.779
23    I        -0.779  -0.779  -0.779  -1.083  -1.083  -1.083  -0.779  -0.779  -0.779
24    V        -0.779  -0.779  -0.779  -0.668  -0.668  -0.668  -0.779  -0.779  -0.779
25    L        -0.779  -0.779  -0.779  -1.033  -1.033  -1.033  -0.779  -0.779  -0.779
26    D        -0.779  -0.779  -0.779  -0.372  -0.372  -0.372  -0.779  -0.779  -0.779
27    F        -0.779  -0.779  -0.779  -0.668  -0.668  -0.668  -0.779  -0.779  -0.779
28    P         1.275   1.275   1.275   1.337   1.337   1.337   1.275   1.275   1.275
29    S         1.275   1.275   1.275   1.167   1.167   1.167   1.275   1.275   1.275
30    F         1.275   1.275   1.275   1.421   1.421   1.421   1.275   1.275   1.275
31    L        -0.779  -0.779  -0.779  -0.823  -0.823  -0.823  -0.779  -0.779  -0.779
32    V        -0.779  -0.779  -0.779  -0.823  -0.823  -0.823  -0.779  -0.779  -0.779
33    G         1.275   1.275   1.275   1.188   1.188   1.188   1.275   1.275   1.275
34    C        -0.779  -0.779  -0.779  -0.316  -0.316  -0.316  -0.779  -0.779  -0.779
35    V        -0.779  -0.779  -0.779  -0.823  -0.823  -0.823  -0.779  -0.779  -0.779
36    F        -0.779  -0.779  -0.779  -0.714  -0.714  -0.714  -0.779  -0.779  -0.779
37    T        -0.779  -0.779  -0.779  -1.000  -1.000  -1.000  -0.779  -0.779  -0.779
38    T        -0.779  -0.779  -0.779  -0.807  -0.807  -0.807  -0.779  -0.779  -0.779
39    M        -0.779  -0.779  -0.779  -0.547  -0.547  -0.547  -0.779  -0.779  -0.779
40    M        -0.779  -0.779  -0.779  -0.592  -0.592  -0.592  -0.779  -0.779  -0.779
41    G         1.275   1.275   1.275   1.188   1.188   1.188   1.275   1.275   1.275
42    P         1.275   1.275   1.275   1.337   1.337   1.337   1.275   1.275   1.275
43    I         1.275   1.275   1.275   0.924   0.924   0.924   1.275   1.275   1.275
44    L         1.275   1.275   1.275   1.274   1.274   1.274   1.275   1.275   1.275
45    Q        -0.779  -0.779  -0.779  -0.607  -0.607  -0.607  -0.779  -0.779  -0.779
46    K        -0.779  -0.779  -0.779  -0.839  -0.839  -0.839  -0.779  -0.779  -0.779
47    L        -0.779  -0.779  -0.779  -0.823  -0.823  -0.823  -0.779  -0.779  -0.779
48    I         1.275   1.275   1.275   0.924   0.924   0.924   1.275   1.275   1.275
49    G         1.275   1.275   1.275   1.188   1.188   1.188   1.275   1.275   1.275
50    K        -0.779  -0.779  -0.779  -0.935  -0.935  -0.935  -0.779  -0.779  -0.779
51    L        -0.779  -0.779  -0.779  -1.033  -1.033  -1.033  -0.779  -0.779  -0.779
52    L        -0.779  -0.779  -0.779  -0.503  -0.503  -0.503  -0.779  -0.779  -0.779
53    V         1.275   1.275   1.275   1.210   1.210   1.210   1.275   1.275   1.275
54    G         1.275   1.275   1.275   1.188   1.188   1.188   1.275   1.275   1.275
55    L         1.275   1.275   1.275   1.274   1.274   1.274   1.275   1.275   1.275
56    I         1.275   1.275   1.275   0.924   0.924   0.924   1.275   1.275   1.275
57    T        -0.779  -0.779  -0.779  -0.744  -0.744  -0.744  -0.779  -0.779  -0.779
58    V        -0.779  -0.779  -0.779  -0.714  -0.714  -0.714  -0.779  -0.779  -0.779
59    C        -0.779  -0.779  -0.779  -0.562  -0.562  -0.562  -0.779  -0.779  -0.779
60    K         1.275   1.275   1.275   1.145   1.145   1.145   1.275   1.275   1.275
61    F         1.275   1.275   1.275   1.421   1.421   1.421   1.275   1.275   1.275
62    L        -0.779  -0.779  -0.779  -0.592  -0.592  -0.592  -0.779  -0.779  -0.779
63    V         1.275   1.275   1.275   1.210   1.210   1.210   1.275   1.275   1.275
64    I        -0.779  -0.779  -0.779  -1.083  -1.083  -1.083  -0.779  -0.779  -0.779
65    I         1.275   1.275   1.275   0.924   0.924   0.924   1.275   1.275   1.275
66    G         1.275   1.275   1.275   1.188   1.188   1.188   1.275   1.275   1.275
67    S        -0.779  -0.779  -0.779  -1.117  -1.117  -1.117  -0.779  -0.779  -0.779
68    I        -0.779  -0.779  -0.779  -0.839  -0.839  -0.839  -0.779  -0.779  -0.779
69    V        -0.779  -0.779  -0.779  -0.823  -0.823  -0.823  -0.779  -0.779  -0.779
70    F        -0.779  -0.779  -0.779  -0.637  -0.637  -0.637  -0.779  -0.779  -0.779
71    V        -0.779  -0.779  -0.779  -1.083  -1.083  -1.083  -0.779  -0.779  -0.779
72    I         1.275   1.275   1.275   0.924   0.924   0.924   1.275   1.275   1.275
73    G        -0.779  -0.779  -0.779  -0.562  -0.562  -0.562  -0.779  -0.779  -0.779
74    V        -0.779  -0.779  -0.779  -1.083  -1.083  -1.083  -0.779  -0.779  -0.779
75    A        -0.779  -0.779  -0.779  -0.592  -0.592  -0.592  -0.779  -0.779  -0.779
76    S         1.275   1.275   1.275   1.167   1.167   1.167   1.275   1.275   1.275
77    K        -0.779  -0.779  -0.779  -0.935  -0.935  -0.935  -0.779  -0.779  -0.779
78    K        -0.779  -0.779  -0.779  -0.951  -0.951  -0.951  -0.779  -0.779  -0.779
79    Y        -0.779  -0.779  -0.779  -0.372  -0.372  -0.372  -0.779  -0.779  -0.779
80    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    K         1.275   1.275   1.275   1.145   1.145   1.145   1.275   1.275   1.275
86    V        -0.779  -0.779  -0.779  -0.760  -0.760  -0.760  -0.779  -0.779  -0.779
87    S        -0.779  -0.779  -0.779  -0.592  -0.592  -0.592  -0.779  -0.779  -0.779
88    I        -0.779  -0.779  -0.779  -1.083  -1.083  -1.083  -0.779  -0.779  -0.779
89    K         1.275   1.275   1.275   1.145   1.145   1.145   1.275   1.275   1.275
90    R         1.275   1.275   1.275   1.358   1.358   1.358   1.275   1.275   1.275
91    S         1.275   1.275   1.275   1.167   1.167   1.167   1.275   1.275   1.275
92    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   M        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   E        -0.779  -0.779  -0.779  -0.791  -0.791  -0.791  -0.779  -0.779  -0.779
104   P         1.275   1.275   1.275   1.337   1.337   1.337   1.275   1.275   1.275
105   K        -0.779  -0.779  -0.779  -0.839  -0.839  -0.839  -0.779  -0.779  -0.779
106   R        -0.779  -0.779  -0.779  -0.562  -0.562  -0.562  -0.779  -0.779  -0.779
107   T         1.275   1.275   1.275   1.316   1.316   1.316   1.275   1.275   1.275
108   A        -0.779  -0.779  -0.779  -0.518  -0.518  -0.518  -0.779  -0.779  -0.779
109   K        -0.779  -0.779  -0.779  -0.839  -0.839  -0.839  -0.779  -0.779  -0.779
110   T        -0.779  -0.779  -0.779  -1.000  -1.000  -1.000  -0.779  -0.779  -0.779
111   A        -0.779  -0.779  -0.779  -0.430  -0.430  -0.430  -0.779  -0.779  -0.779
112   T        -0.779  -0.779  -0.779  -0.839  -0.839  -0.839  -0.779  -0.779  -0.779
113   V        -0.779  -0.779  -0.779  -1.083  -1.083  -1.083  -0.779  -0.779  -0.779
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   P         1.275   1.275   1.275   1.337   1.337   1.337   1.275   1.275   1.275
116   M        -0.779  -0.779  -0.779  -0.302  -0.302  -0.302  -0.779  -0.779  -0.779
117   E         1.275   1.275   1.275   1.379   1.379   1.379   1.275   1.275   1.275
118   K        -0.779  -0.779  -0.779  -0.744  -0.744  -0.744  -0.779  -0.779  -0.779
119   D        -0.779  -0.779  -0.779  -0.729  -0.729  -0.729  -0.779  -0.779  -0.779
120   E         1.275   1.275   1.275   1.379   1.379   1.379   1.275   1.275   1.275
121   G        -0.779  -0.779  -0.779  -0.652  -0.652  -0.652  -0.779  -0.779  -0.779
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   V        -0.779  -0.779  -0.779  -1.083  -1.083  -1.083  -0.779  -0.779  -0.779
124   G         1.275   1.275   1.275   1.188   1.188   1.188   1.275   1.275   1.275
125   S         1.275   1.275   1.275   1.167   1.167   1.167   1.275   1.275   1.275
126   Y         1.275   1.275   1.275   1.483   1.483   1.483   1.275   1.275   1.275
127   N        -0.779  -0.779  -0.779  -0.698  -0.698  -0.698  -0.779  -0.779  -0.779
128   Y         1.275   1.275   1.275   1.483   1.483   1.483   1.275   1.275   1.275
129   F         1.275   1.275   1.275   1.421   1.421   1.421   1.275   1.275   1.275
130   E        -0.779  -0.779  -0.779  -0.532  -0.532  -0.532  -0.779  -0.779  -0.779
131   I         1.275   1.275   1.275   0.924   0.924   0.924   1.275   1.275   1.275
132   P         1.275   1.275   1.275   1.337   1.337   1.337   1.275   1.275   1.275
133   I        -0.779  -0.779  -0.779  -1.083  -1.083  -1.083  -0.779  -0.779  -0.779
134   T        -0.779  -0.779  -0.779  -0.668  -0.668  -0.668  -0.779  -0.779  -0.779
135   K         1.275   1.275   1.275   1.145   1.145   1.145   1.275   1.275   1.275
136   E         1.275   1.275   1.275   1.379   1.379   1.379   1.275   1.275   1.275
137   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   P         1.275   1.275   1.275   1.337   1.337   1.337   1.275   1.275   1.275
142   Y         1.275   1.275   1.275   1.483   1.483   1.483   1.275   1.275   1.275
143   I         1.275   1.275   1.275   0.924   0.924   0.924   1.275   1.275   1.275
144   N        -0.779  -0.779  -0.779  -0.698  -0.698  -0.698  -0.779  -0.779  -0.779
145   C        -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   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
151   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
152   R         1.275   1.275   1.275   1.358   1.358   1.358   1.275   1.275   1.275
153   K         1.275   1.275   1.275   1.145   1.145   1.145   1.275   1.275   1.275
154   P         1.275   1.275   1.275   1.337   1.337   1.337   1.275   1.275   1.275
155   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
156   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
157   G        -0.779  -0.779  -0.779  -0.919  -0.919  -0.919  -0.779  -0.779  -0.779
158   P        -0.779  -0.779  -0.779  -0.984  -0.984  -0.984  -0.779  -0.779  -0.779
159   S         1.275   1.275   1.275   1.167   1.167   1.167   1.275   1.275   1.275
160   S        -0.779  -0.779  -0.779  -0.823  -0.823  -0.823  -0.779  -0.779  -0.779
161   V        -0.779  -0.779  -0.779  -1.083  -1.083  -1.083  -0.779  -0.779  -0.779
162   G        -0.779  -0.779  -0.779  -0.919  -0.919  -0.919  -0.779  -0.779  -0.779
163   L        -0.779  -0.779  -0.779  -1.033  -1.033  -1.033  -0.779  -0.779  -0.779
164   S        -0.779  -0.779  -0.779  -0.729  -0.729  -0.729  -0.779  -0.779  -0.779
165   N        -0.779  -0.779  -0.779  -0.532  -0.532  -0.532  -0.779  -0.779  -0.779
166   S        -0.779  -0.779  -0.779  -0.951  -0.951  -0.951  -0.779  -0.779  -0.779
167   N        -0.779  -0.779  -0.779  -0.488  -0.488  -0.488  -0.779  -0.779  -0.779
168   R        -0.779  -0.779  -0.779  -0.714  -0.714  -0.714  -0.779  -0.779  -0.779
169   Y         1.275   1.275   1.275   1.483   1.483   1.483   1.275   1.275   1.275
170   E        -0.779  -0.779  -0.779  -0.668  -0.668  -0.668  -0.779  -0.779  -0.779
171   N         1.275   1.275   1.275   1.503   1.503   1.503   1.275   1.275   1.275
172   F         1.275   1.275   1.275   1.421   1.421   1.421   1.275   1.275   1.275
173   I        -0.779  -0.779  -0.779  -1.083  -1.083  -1.083  -0.779  -0.779  -0.779
174   N        -0.779  -0.779  -0.779  -0.547  -0.547  -0.547  -0.779  -0.779  -0.779
175   M        -0.779  -0.779  -0.779  -0.637  -0.637  -0.637  -0.779  -0.779  -0.779
176   A         1.275   1.275   1.275   1.524   1.524   1.524   1.275   1.275   1.275
177   R         1.275   1.275   1.275   1.358   1.358   1.358   1.275   1.275   1.275
178   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   K        -0.779  -0.779  -0.779  -0.807  -0.807  -0.807  -0.779  -0.779  -0.779
* 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/Q12274
Output conservation file - output/Q12274
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
