1     M         1.310   1.310   1.310   1.577   1.577   1.577   1.310   1.310   1.310
2     D        -0.758  -0.758  -0.758  -1.003  -1.003  -1.003  -0.758  -0.758  -0.758
3     G        -0.758  -0.758  -0.758  -0.597  -0.597  -0.597  -0.758  -0.758  -0.758
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     L         1.310   1.310   1.310   1.157   1.157   1.157   1.310   1.310   1.310
6     S        -0.758  -0.758  -0.758  -0.582  -0.582  -0.582  -0.758  -0.758  -0.758
7     F         1.310   1.310   1.310   1.618   1.618   1.618   1.310   1.310   1.310
8     V         1.310   1.310   1.310   1.264   1.264   1.264   1.310   1.310   1.310
9     D         1.310   1.310   1.310   1.091   1.091   1.091   1.310   1.310   1.310
10    K        -0.758  -0.758  -0.758  -0.922  -0.922  -0.922  -0.758  -0.758  -0.758
11    G        -0.758  -0.758  -0.758  -0.657  -0.657  -0.657  -0.758  -0.758  -0.758
12    K        -0.758  -0.758  -0.758  -0.734  -0.734  -0.734  -0.758  -0.758  -0.758
13    I        -0.758  -0.758  -0.758  -0.843  -0.843  -0.843  -0.758  -0.758  -0.758
14    P        -0.758  -0.758  -0.758  -0.796  -0.796  -0.796  -0.758  -0.758  -0.758
15    D        -0.758  -0.758  -0.758  -0.874  -0.874  -0.874  -0.758  -0.758  -0.758
16    G        -0.758  -0.758  -0.758  -0.657  -0.657  -0.657  -0.758  -0.758  -0.758
17    Y        -0.758  -0.758  -0.758  -0.479  -0.479  -0.479  -0.758  -0.758  -0.758
18    K        -0.758  -0.758  -0.758  -0.827  -0.827  -0.827  -0.758  -0.758  -0.758
19    N        -0.758  -0.758  -0.758  -0.672  -0.672  -0.672  -0.758  -0.758  -0.758
20    E        -0.758  -0.758  -0.758  -0.567  -0.567  -0.567  -0.758  -0.758  -0.758
21    I        -0.758  -0.758  -0.758  -0.843  -0.843  -0.843  -0.758  -0.758  -0.758
22    D         1.310   1.310   1.310   1.091   1.091   1.091   1.310   1.310   1.310
23    Q        -0.758  -0.758  -0.758  -0.780  -0.780  -0.780  -0.758  -0.758  -0.758
24    L         1.310   1.310   1.310   1.157   1.157   1.157   1.310   1.310   1.310
25    V         1.310   1.310   1.310   1.264   1.264   1.264   1.310   1.310   1.310
26    K        -0.758  -0.758  -0.758  -0.827  -0.827  -0.827  -0.758  -0.758  -0.758
27    K        -0.758  -0.758  -0.758  -0.827  -0.827  -0.827  -0.758  -0.758  -0.758
28    E         1.310   1.310   1.310   1.221   1.221   1.221   1.310   1.310   1.310
29    F        -0.758  -0.758  -0.758  -0.307  -0.307  -0.307  -0.758  -0.758  -0.758
30    A        -0.758  -0.758  -0.758  -0.657  -0.657  -0.657  -0.758  -0.758  -0.758
31    N        -0.758  -0.758  -0.758  -0.672  -0.672  -0.672  -0.758  -0.758  -0.758
32    I        -0.758  -0.758  -0.758  -0.612  -0.612  -0.612  -0.758  -0.758  -0.758
33    K        -0.758  -0.758  -0.758  -0.627  -0.627  -0.627  -0.758  -0.758  -0.758
34    R        -0.758  -0.758  -0.758  -0.827  -0.827  -0.827  -0.758  -0.758  -0.758
35    E         1.310   1.310   1.310   1.221   1.221   1.221   1.310   1.310   1.310
36    P        -0.758  -0.758  -0.758  -0.553  -0.553  -0.553  -0.758  -0.758  -0.758
37    V        -0.758  -0.758  -0.758  -0.734  -0.734  -0.734  -0.758  -0.758  -0.758
38    H         1.310   1.310   1.310   1.638   1.638   1.638   1.310   1.310   1.310
39    P         1.310   1.310   1.310   1.495   1.495   1.495   1.310   1.310   1.310
40    E         1.310   1.310   1.310   1.221   1.221   1.221   1.310   1.310   1.310
41    I        -0.758  -0.758  -0.758  -0.843  -0.843  -0.843  -0.758  -0.758  -0.758
42    R        -0.758  -0.758  -0.758  -0.749  -0.749  -0.749  -0.758  -0.758  -0.758
43    G        -0.758  -0.758  -0.758  -0.796  -0.796  -0.796  -0.758  -0.758  -0.758
44    I        -0.758  -0.758  -0.758  -0.843  -0.843  -0.843  -0.758  -0.758  -0.758
45    L        -0.758  -0.758  -0.758  -0.688  -0.688  -0.688  -0.758  -0.758  -0.758
46    A         1.310   1.310   1.310   1.349   1.349   1.349   1.310   1.310   1.310
47    K        -0.758  -0.758  -0.758  -0.734  -0.734  -0.734  -0.758  -0.758  -0.758
48    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    K         1.310   1.310   1.310   1.328   1.328   1.328   1.310   1.310   1.310
50    G         1.310   1.310   1.310   1.433   1.433   1.433   1.310   1.310   1.310
51    A        -0.758  -0.758  -0.758  -0.858  -0.858  -0.858  -0.758  -0.758  -0.758
52    D         1.310   1.310   1.310   1.091   1.091   1.091   1.310   1.310   1.310
53    N        -0.758  -0.758  -0.758  -0.672  -0.672  -0.672  -0.758  -0.758  -0.758
54    S        -0.758  -0.758  -0.758  -0.780  -0.780  -0.780  -0.758  -0.758  -0.758
55    V        -0.758  -0.758  -0.758  -0.749  -0.749  -0.749  -0.758  -0.758  -0.758
56    S        -0.758  -0.758  -0.758  -0.627  -0.627  -0.627  -0.758  -0.758  -0.758
57    T        -0.758  -0.758  -0.758  -0.597  -0.597  -0.597  -0.758  -0.758  -0.758
58    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    N        -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    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    I         1.310   1.310   1.310   1.264   1.264   1.264   1.310   1.310   1.310
100   D         1.310   1.310   1.310   1.091   1.091   1.091   1.310   1.310   1.310
101   T        -0.758  -0.758  -0.758  -0.796  -0.796  -0.796  -0.758  -0.758  -0.758
102   S        -0.758  -0.758  -0.758  -0.688  -0.688  -0.688  -0.758  -0.758  -0.758
103   R         1.310   1.310   1.310   1.157   1.157   1.157   1.310   1.310   1.310
104   Y         1.310   1.310   1.310   1.412   1.412   1.412   1.310   1.310   1.310
105   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   N         1.310   1.310   1.310   1.412   1.412   1.412   1.310   1.310   1.310
108   E        -0.758  -0.758  -0.758  -1.003  -1.003  -1.003  -0.758  -0.758  -0.758
109   S        -0.758  -0.758  -0.758  -0.688  -0.688  -0.688  -0.758  -0.758  -0.758
110   S        -0.758  -0.758  -0.758  -0.627  -0.627  -0.627  -0.758  -0.758  -0.758
111   E        -0.758  -0.758  -0.758  -1.003  -1.003  -1.003  -0.758  -0.758  -0.758
112   V         1.310   1.310   1.310   1.264   1.264   1.264   1.310   1.310   1.310
113   S        -0.758  -0.758  -0.758  -0.827  -0.827  -0.827  -0.758  -0.758  -0.758
114   L         1.310   1.310   1.310   1.157   1.157   1.157   1.310   1.310   1.310
115   L         1.310   1.310   1.310   1.157   1.157   1.157   1.310   1.310   1.310
116   G        -0.758  -0.758  -0.758  -0.672  -0.672  -0.672  -0.758  -0.758  -0.758
117   I         1.310   1.310   1.310   1.264   1.264   1.264   1.310   1.310   1.310
118   V         1.310   1.310   1.310   1.264   1.264   1.264   1.310   1.310   1.310
119   D         1.310   1.310   1.310   1.091   1.091   1.091   1.310   1.310   1.310
120   S         1.310   1.310   1.310   1.391   1.391   1.391   1.310   1.310   1.310
121   Y         1.310   1.310   1.310   1.412   1.412   1.412   1.310   1.310   1.310
122   L         1.310   1.310   1.310   1.157   1.157   1.157   1.310   1.310   1.310
123   K        -0.758  -0.758  -0.758  -0.874  -0.874  -0.874  -0.758  -0.758  -0.758
124   H         1.310   1.310   1.310   1.638   1.638   1.638   1.310   1.310   1.310
125   Q        -0.758  -0.758  -0.758  -0.688  -0.688  -0.688  -0.758  -0.758  -0.758
126   E         1.310   1.310   1.310   1.221   1.221   1.221   1.310   1.310   1.310
127   I         1.310   1.310   1.310   1.264   1.264   1.264   1.310   1.310   1.310
128   V        -0.758  -0.758  -0.758  -0.718  -0.718  -0.718  -0.758  -0.758  -0.758
129   L         1.310   1.310   1.310   1.157   1.157   1.157   1.310   1.310   1.310
130   D        -0.758  -0.758  -0.758  -1.053  -1.053  -1.053  -0.758  -0.758  -0.758
131   T        -0.758  -0.758  -0.758  -0.749  -0.749  -0.749  -0.758  -0.758  -0.758
132   L         1.310   1.310   1.310   1.157   1.157   1.157   1.310   1.310   1.310
133   L        -0.758  -0.758  -0.758  -0.922  -0.922  -0.922  -0.758  -0.758  -0.758
134   P        -0.758  -0.758  -0.758  -0.582  -0.582  -0.582  -0.758  -0.758  -0.758
135   Q        -0.758  -0.758  -0.758  -0.703  -0.703  -0.703  -0.758  -0.758  -0.758
136   T         1.310   1.310   1.310   1.433   1.433   1.433   1.310   1.310   1.310
137   V        -0.758  -0.758  -0.758  -0.843  -0.843  -0.843  -0.758  -0.758  -0.758
138   S        -0.758  -0.758  -0.758  -0.749  -0.749  -0.749  -0.758  -0.758  -0.758
139   N         1.310   1.310   1.310   1.412   1.412   1.412   1.310   1.310   1.310
140   Q         1.310   1.310   1.310   1.391   1.391   1.391   1.310   1.310   1.310
141   W         1.310   1.310   1.310   1.678   1.678   1.678   1.310   1.310   1.310
142   R        -0.758  -0.758  -0.758  -0.922  -0.922  -0.922  -0.758  -0.758  -0.758
143   I         1.310   1.310   1.310   1.264   1.264   1.264   1.310   1.310   1.310
144   N        -0.758  -0.758  -0.758  -0.642  -0.642  -0.642  -0.758  -0.758  -0.758
145   N         1.310   1.310   1.310   1.412   1.412   1.412   1.310   1.310   1.310
146   D         1.310   1.310   1.310   1.091   1.091   1.091   1.310   1.310   1.310
147   Y        -0.758  -0.758  -0.758  -0.450  -0.450  -0.450  -0.758  -0.758  -0.758
148   I        -0.758  -0.758  -0.758  -0.749  -0.749  -0.749  -0.758  -0.758  -0.758
149   R        -0.758  -0.758  -0.758  -0.827  -0.827  -0.827  -0.758  -0.758  -0.758
150   Q        -0.758  -0.758  -0.758  -0.657  -0.657  -0.657  -0.758  -0.758  -0.758
151   T        -0.758  -0.758  -0.758  -0.657  -0.657  -0.657  -0.758  -0.758  -0.758
152   C        -0.758  -0.758  -0.758  -0.465  -0.465  -0.465  -0.758  -0.758  -0.758
153   T        -0.758  -0.758  -0.758  -0.597  -0.597  -0.597  -0.758  -0.758  -0.758
154   I        -0.758  -0.758  -0.758  -0.843  -0.843  -0.843  -0.758  -0.758  -0.758
155   V        -0.758  -0.758  -0.758  -0.612  -0.612  -0.612  -0.758  -0.758  -0.758
156   E        -0.758  -0.758  -0.758  -0.780  -0.780  -0.780  -0.758  -0.758  -0.758
157   E        -0.758  -0.758  -0.758  -0.811  -0.811  -0.811  -0.758  -0.758  -0.758
158   M        -0.758  -0.758  -0.758  -0.494  -0.494  -0.494  -0.758  -0.758  -0.758
159   N        -0.758  -0.758  -0.758  -0.734  -0.734  -0.734  -0.758  -0.758  -0.758
160   I        -0.758  -0.758  -0.758  -0.971  -0.971  -0.971  -0.758  -0.758  -0.758
161   Q        -0.758  -0.758  -0.758  -0.703  -0.703  -0.703  -0.758  -0.758  -0.758
162   Q        -0.758  -0.758  -0.758  -0.827  -0.827  -0.827  -0.758  -0.758  -0.758
163   R        -0.758  -0.758  -0.758  -0.827  -0.827  -0.827  -0.758  -0.758  -0.758
164   K        -0.758  -0.758  -0.758  -0.672  -0.672  -0.672  -0.758  -0.758  -0.758
165   Q         1.310   1.310   1.310   1.391   1.391   1.391   1.310   1.310   1.310
166   I        -0.758  -0.758  -0.758  -0.922  -0.922  -0.922  -0.758  -0.758  -0.758
167   N        -0.758  -0.758  -0.758  -0.858  -0.858  -0.858  -0.758  -0.758  -0.758
168   D        -0.758  -0.758  -0.758  -0.906  -0.906  -0.906  -0.758  -0.758  -0.758
169   L         1.310   1.310   1.310   1.157   1.157   1.157   1.310   1.310   1.310
170   E         1.310   1.310   1.310   1.221   1.221   1.221   1.310   1.310   1.310
171   I        -0.758  -0.758  -0.758  -0.796  -0.796  -0.796  -0.758  -0.758  -0.758
172   Y         1.310   1.310   1.310   1.412   1.412   1.412   1.310   1.310   1.310
173   R         1.310   1.310   1.310   1.157   1.157   1.157   1.310   1.310   1.310
174   K        -0.758  -0.758  -0.758  -0.874  -0.874  -0.874  -0.758  -0.758  -0.758
175   R        -0.758  -0.758  -0.758  -1.053  -1.053  -1.053  -0.758  -0.758  -0.758
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   L        -0.758  -0.758  -0.758  -0.922  -0.922  -0.922  -0.758  -0.758  -0.758
* 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/Q06091
Output conservation file - output/Q06091
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
