1     M         1.527   1.527   1.527   1.927   1.927   1.927   1.527   1.527   1.527
2     L         1.527   1.527   1.527   1.036   1.036   1.036   1.527   1.527   1.527
3     Y        -0.651  -0.651  -0.651  -0.400  -0.400  -0.400  -0.651  -0.651  -0.651
4     T         1.527   1.527   1.527   1.506   1.506   1.506   1.527   1.527   1.527
5     R        -0.651  -0.651  -0.651  -0.314  -0.314  -0.314  -0.651  -0.651  -0.651
6     L        -0.651  -0.651  -0.651  -0.869  -0.869  -0.869  -0.651  -0.651  -0.651
7     L         1.527   1.527   1.527   1.036   1.036   1.036   1.527   1.527   1.527
8     R         1.527   1.527   1.527   1.809   1.809   1.809   1.527   1.527   1.527
9     H        -0.651  -0.651  -0.651  -0.244  -0.244  -0.244  -0.651  -0.651  -0.651
10    N        -0.651  -0.651  -0.651  -0.790  -0.790  -0.790  -0.651  -0.651  -0.651
11    S        -0.651  -0.651  -0.651  -0.728  -0.728  -0.728  -0.651  -0.651  -0.651
12    Q        -0.651  -0.651  -0.651  -0.343  -0.343  -0.343  -0.651  -0.651  -0.651
13    F        -0.651  -0.651  -0.651  -0.386  -0.386  -0.386  -0.651  -0.651  -0.651
14    T        -0.651  -0.651  -0.651  -0.713  -0.713  -0.713  -0.651  -0.651  -0.651
15    K        -0.651  -0.651  -0.651  -0.591  -0.591  -0.591  -0.651  -0.651  -0.651
16    F        -0.651  -0.651  -0.651  -0.400  -0.400  -0.400  -0.651  -0.651  -0.651
17    S        -0.651  -0.651  -0.651  -0.790  -0.790  -0.790  -0.651  -0.651  -0.651
18    G        -0.651  -0.651  -0.651  -0.531  -0.531  -0.531  -0.651  -0.651  -0.651
19    T        -0.651  -0.651  -0.651  -0.473  -0.473  -0.473  -0.651  -0.651  -0.651
20    S         1.527   1.527   1.527   1.167   1.167   1.167   1.527   1.527   1.527
21    P         1.527   1.527   1.527   1.750   1.750   1.750   1.527   1.527   1.527
22    N         1.527   1.527   1.527   1.670   1.670   1.670   1.527   1.527   1.527
23    L        -0.651  -0.651  -0.651  -0.999  -0.999  -0.999  -0.651  -0.651  -0.651
24    G        -0.651  -0.651  -0.651  -0.790  -0.790  -0.790  -0.651  -0.651  -0.651
25    S         1.527   1.527   1.527   1.167   1.167   1.167   1.527   1.527   1.527
26    K         1.527   1.527   1.527   1.444   1.444   1.444   1.527   1.527   1.527
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    P        -0.651  -0.651  -0.651  -0.371  -0.371  -0.371  -0.651  -0.651  -0.651
37    L        -0.651  -0.651  -0.651  -0.999  -0.999  -0.999  -0.651  -0.651  -0.651
38    F        -0.651  -0.651  -0.651  -0.343  -0.343  -0.343  -0.651  -0.651  -0.651
39    S        -0.651  -0.651  -0.651  -0.917  -0.917  -0.917  -0.651  -0.651  -0.651
40    K         1.527   1.527   1.527   1.444   1.444   1.444   1.527   1.527   1.527
41    G        -0.651  -0.651  -0.651  -0.790  -0.790  -0.790  -0.651  -0.651  -0.651
42    N         1.527   1.527   1.527   1.670   1.670   1.670   1.527   1.527   1.527
43    L        -0.651  -0.651  -0.651  -0.999  -0.999  -0.999  -0.651  -0.651  -0.651
44    Y        -0.651  -0.651  -0.651  -0.371  -0.371  -0.371  -0.651  -0.651  -0.651
45    T        -0.651  -0.651  -0.651  -0.651  -0.651  -0.651  -0.651  -0.651  -0.651
46    S        -0.651  -0.651  -0.651  -0.790  -0.790  -0.790  -0.651  -0.651  -0.651
47    L         1.527   1.527   1.527   1.036   1.036   1.036   1.527   1.527   1.527
48    L        -0.651  -0.651  -0.651  -0.999  -0.999  -0.999  -0.651  -0.651  -0.651
49    V         1.527   1.527   1.527   1.527   1.527   1.527   1.527   1.527   1.527
50    T        -0.651  -0.651  -0.651  -0.546  -0.546  -0.546  -0.651  -0.651  -0.651
51    T        -0.651  -0.651  -0.651  -0.917  -0.917  -0.917  -0.651  -0.651  -0.651
52    L         1.527   1.527   1.527   1.036   1.036   1.036   1.527   1.527   1.527
53    Y        -0.651  -0.651  -0.651  -0.400  -0.400  -0.400  -0.651  -0.651  -0.651
54    G        -0.651  -0.651  -0.651  -0.371  -0.371  -0.371  -0.651  -0.651  -0.651
55    T        -0.651  -0.651  -0.651  -1.015  -1.015  -1.015  -0.651  -0.651  -0.651
56    G         1.527   1.527   1.527   1.670   1.670   1.670   1.527   1.527   1.527
57    L         1.527   1.527   1.527   1.036   1.036   1.036   1.527   1.527   1.527
58    A        -0.651  -0.651  -0.651  -0.371  -0.371  -0.371  -0.651  -0.651  -0.651
59    C         1.527   1.527   1.527   1.985   1.985   1.985   1.527   1.527   1.527
60    L         1.527   1.527   1.527   1.036   1.036   1.036   1.527   1.527   1.527
61    Y         1.527   1.527   1.527   1.670   1.670   1.670   1.527   1.527   1.527
62    L        -0.651  -0.651  -0.651  -1.065  -1.065  -1.065  -0.651  -0.651  -0.651
63    E        -0.651  -0.651  -0.651  -0.286  -0.286  -0.286  -0.651  -0.651  -0.651
64    S        -0.651  -0.651  -0.651  -0.790  -0.790  -0.790  -0.651  -0.651  -0.651
65    N        -0.651  -0.651  -0.651  -0.546  -0.546  -0.546  -0.651  -0.651  -0.651
66    S        -0.651  -0.651  -0.651  -0.775  -0.775  -0.775  -0.651  -0.651  -0.651
67    L        -0.651  -0.651  -0.651  -1.015  -1.015  -1.015  -0.651  -0.651  -0.651
68    N        -0.651  -0.651  -0.651  -0.591  -0.591  -0.591  -0.651  -0.651  -0.651
69    K        -0.651  -0.651  -0.651  -0.576  -0.576  -0.576  -0.651  -0.651  -0.651
70    S        -0.651  -0.651  -0.651  -0.682  -0.682  -0.682  -0.651  -0.651  -0.651
71    K        -0.651  -0.651  -0.651  -0.591  -0.591  -0.591  -0.651  -0.651  -0.651
72    E         1.527   1.527   1.527   1.770   1.770   1.770   1.527   1.527   1.527
73    Q        -0.651  -0.651  -0.651  -0.775  -0.775  -0.775  -0.651  -0.651  -0.651
74    E        -0.651  -0.651  -0.651  -0.473  -0.473  -0.473  -0.651  -0.651  -0.651
75    D        -0.651  -0.651  -0.651  -0.357  -0.357  -0.357  -0.651  -0.651  -0.651
76    P        -0.651  -0.651  -0.651  -0.487  -0.487  -0.487  -0.651  -0.651  -0.651
77    H        -0.651  -0.651  -0.651  -0.357  -0.357  -0.357  -0.651  -0.651  -0.651
78    A        -0.651  -0.651  -0.651  -0.531  -0.531  -0.531  -0.651  -0.651  -0.651
79    I         1.527   1.527   1.527   1.690   1.690   1.690   1.527   1.527   1.527
80    A        -0.651  -0.651  -0.651  -0.357  -0.357  -0.357  -0.651  -0.651  -0.651
81    E        -0.651  -0.651  -0.651  -0.286  -0.286  -0.286  -0.651  -0.651  -0.651
82    D        -0.651  -0.651  -0.651  -0.343  -0.343  -0.343  -0.651  -0.651  -0.651
83    D        -0.651  -0.651  -0.651  -0.300  -0.300  -0.300  -0.651  -0.651  -0.651
84    I        -0.651  -0.651  -0.651  -0.775  -0.775  -0.775  -0.651  -0.651  -0.651
85    V        -0.651  -0.651  -0.651  -0.531  -0.531  -0.531  -0.651  -0.651  -0.651
86    N        -0.651  -0.651  -0.651  -0.591  -0.591  -0.591  -0.651  -0.651  -0.651
87    I        -0.651  -0.651  -0.651  -0.517  -0.517  -0.517  -0.651  -0.651  -0.651
88    V        -0.651  -0.651  -0.651  -0.901  -0.901  -0.901  -0.651  -0.651  -0.651
89    H        -0.651  -0.651  -0.651  -0.606  -0.606  -0.606  -0.651  -0.651  -0.651
90    D        -0.651  -0.651  -0.651  -0.517  -0.517  -0.517  -0.651  -0.651  -0.651
91    A        -0.651  -0.651  -0.651  -0.300  -0.300  -0.300  -0.651  -0.651  -0.651
92    P         1.527   1.527   1.527   1.750   1.750   1.750   1.527   1.527   1.527
93    N        -0.651  -0.651  -0.651  -0.790  -0.790  -0.790  -0.651  -0.651  -0.651
94    R        -0.651  -0.651  -0.651  -0.258  -0.258  -0.258  -0.651  -0.651  -0.651
95    I         1.527   1.527   1.527   1.690   1.690   1.690   1.527   1.527   1.527
96    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
100   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   D        -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   Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   L        -0.651  -0.651  -0.651  -0.869  -0.869  -0.869  -0.651  -0.651  -0.651
111   Q        -0.651  -0.651  -0.651  -0.414  -0.414  -0.414  -0.651  -0.651  -0.651
112   K        -0.651  -0.651  -0.651  -0.531  -0.531  -0.531  -0.651  -0.651  -0.651
113   S         1.527   1.527   1.527   1.167   1.167   1.167   1.527   1.527   1.527
114   D        -0.651  -0.651  -0.651  -0.473  -0.473  -0.473  -0.651  -0.651  -0.651
115   L        -0.651  -0.651  -0.651  -0.853  -0.853  -0.853  -0.651  -0.651  -0.651
116   H        -0.651  -0.651  -0.651  -0.202  -0.202  -0.202  -0.651  -0.651  -0.651
117   K        -0.651  -0.651  -0.651  -1.065  -1.065  -1.065  -0.651  -0.651  -0.651
118   V         1.527   1.527   1.527   1.527   1.527   1.527   1.527   1.527   1.527
119   L         1.527   1.527   1.527   1.036   1.036   1.036   1.527   1.527   1.527
120   H         1.527   1.527   1.527   1.907   1.907   1.907   1.527   1.527   1.527
121   S         1.527   1.527   1.527   1.167   1.167   1.167   1.527   1.527   1.527
122   L         1.527   1.527   1.527   1.036   1.036   1.036   1.527   1.527   1.527
123   T         1.527   1.527   1.527   1.506   1.506   1.506   1.527   1.527   1.527
124   Y         1.527   1.527   1.527   1.670   1.670   1.670   1.527   1.527   1.527
125   S        -0.651  -0.651  -0.651  -0.682  -0.682  -0.682  -0.651  -0.651  -0.651
126   D         1.527   1.527   1.527   1.770   1.770   1.770   1.527   1.527   1.527
127   V        -0.651  -0.651  -0.651  -0.999  -0.999  -0.999  -0.651  -0.651  -0.651
128   S         1.527   1.527   1.527   1.167   1.167   1.167   1.527   1.527   1.527
129   Q        -0.651  -0.651  -0.651  -0.357  -0.357  -0.357  -0.651  -0.651  -0.651
130   F        -0.651  -0.651  -0.651  -0.853  -0.853  -0.853  -0.651  -0.651  -0.651
131   S        -0.651  -0.651  -0.651  -0.917  -0.917  -0.917  -0.651  -0.651  -0.651
132   I        -0.651  -0.651  -0.651  -0.517  -0.517  -0.517  -0.651  -0.651  -0.651
133   V        -0.651  -0.651  -0.651  -0.651  -0.651  -0.651  -0.651  -0.651  -0.651
134   W        -0.651  -0.651  -0.651  -0.012  -0.012  -0.012  -0.651  -0.651  -0.651
135   G         1.527   1.527   1.527   1.670   1.670   1.670   1.527   1.527   1.527
136   F         1.527   1.527   1.527   1.710   1.710   1.710   1.527   1.527   1.527
137   L         1.527   1.527   1.527   1.036   1.036   1.036   1.527   1.527   1.527
138   I        -0.651  -0.651  -0.651  -0.414  -0.414  -0.414  -0.651  -0.651  -0.651
139   Q        -0.651  -0.651  -0.651  -0.414  -0.414  -0.414  -0.651  -0.651  -0.651
140   L        -0.651  -0.651  -0.651  -0.869  -0.869  -0.869  -0.651  -0.651  -0.651
141   S        -0.651  -0.651  -0.651  -0.917  -0.917  -0.917  -0.651  -0.651  -0.651
142   S        -0.651  -0.651  -0.651  -0.713  -0.713  -0.713  -0.651  -0.651  -0.651
143   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   I        -0.651  -0.651  -0.651  -0.357  -0.357  -0.357  -0.651  -0.651  -0.651
145   G        -0.651  -0.651  -0.651  -0.371  -0.371  -0.371  -0.651  -0.651  -0.651
146   N        -0.651  -0.651  -0.651  -0.329  -0.329  -0.329  -0.651  -0.651  -0.651
147   S        -0.651  -0.651  -0.651  -0.775  -0.775  -0.775  -0.651  -0.651  -0.651
148   T        -0.651  -0.651  -0.651  -0.917  -0.917  -0.917  -0.651  -0.651  -0.651
149   L        -0.651  -0.651  -0.651  -0.853  -0.853  -0.853  -0.651  -0.651  -0.651
150   G         1.527   1.527   1.527   1.670   1.670   1.670   1.527   1.527   1.527
151   K         1.527   1.527   1.527   1.444   1.444   1.444   1.527   1.527   1.527
152   K         1.527   1.527   1.527   1.444   1.444   1.444   1.527   1.527   1.527
153   S         1.527   1.527   1.527   1.167   1.167   1.167   1.527   1.527   1.527
154   I        -0.651  -0.651  -0.651  -0.869  -0.869  -0.869  -0.651  -0.651  -0.651
155   L        -0.651  -0.651  -0.651  -0.999  -0.999  -0.999  -0.651  -0.651  -0.651
156   Y         1.527   1.527   1.527   1.670   1.670   1.670   1.527   1.527   1.527
157   K        -0.651  -0.651  -0.651  -0.487  -0.487  -0.487  -0.651  -0.651  -0.651
158   G        -0.651  -0.651  -0.651  -0.414  -0.414  -0.414  -0.651  -0.651  -0.651
159   S         1.527   1.527   1.527   1.167   1.167   1.167   1.527   1.527   1.527
160   V        -0.651  -0.651  -0.651  -0.999  -0.999  -0.999  -0.651  -0.651  -0.651
161   V        -0.651  -0.651  -0.651  -0.502  -0.502  -0.502  -0.651  -0.651  -0.651
162   S         1.527   1.527   1.527   1.167   1.167   1.167   1.527   1.527   1.527
163   V        -0.651  -0.651  -0.651  -0.999  -0.999  -0.999  -0.651  -0.651  -0.651
164   L        -0.651  -0.651  -0.651  -0.999  -0.999  -0.999  -0.651  -0.651  -0.651
165   G        -0.651  -0.651  -0.651  -0.885  -0.885  -0.885  -0.651  -0.651  -0.651
166   F         1.527   1.527   1.527   1.710   1.710   1.710   1.527   1.527   1.527
167   P         1.527   1.527   1.527   1.750   1.750   1.750   1.527   1.527   1.527
168   P        -0.651  -0.651  -0.651  -0.487  -0.487  -0.487  -0.651  -0.651  -0.651
169   L        -0.651  -0.651  -0.651  -1.288  -1.288  -1.288  -0.651  -0.651  -0.651
170   I        -0.651  -0.651  -0.651  -0.775  -0.775  -0.775  -0.651  -0.651  -0.651
171   Y         1.527   1.527   1.527   1.670   1.670   1.670   1.527   1.527   1.527
172   M        -0.651  -0.651  -0.651  -0.216  -0.216  -0.216  -0.651  -0.651  -0.651
173   A        -0.651  -0.651  -0.651  -0.822  -0.822  -0.822  -0.651  -0.651  -0.651
174   L        -0.651  -0.651  -0.651  -0.885  -0.885  -0.885  -0.651  -0.651  -0.651
175   K        -0.651  -0.651  -0.651  -0.576  -0.576  -0.576  -0.651  -0.651  -0.651
176   L        -0.651  -0.651  -0.651  -1.288  -1.288  -1.288  -0.651  -0.651  -0.651
177   R         1.527   1.527   1.527   1.809   1.809   1.809   1.527   1.527   1.527
178   M        -0.651  -0.651  -0.651  -0.244  -0.244  -0.244  -0.651  -0.651  -0.651
179   K        -0.651  -0.651  -0.651  -0.517  -0.517  -0.517  -0.651  -0.651  -0.651
180   Q        -0.651  -0.651  -0.651  -0.576  -0.576  -0.576  -0.651  -0.651  -0.651
181   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   E        -0.651  -0.651  -0.651  -0.473  -0.473  -0.473  -0.651  -0.651  -0.651
183   K         1.527   1.527   1.527   1.444   1.444   1.444   1.527   1.527   1.527
184   A        -0.651  -0.651  -0.651  -0.371  -0.371  -0.371  -0.651  -0.651  -0.651
185   G        -0.651  -0.651  -0.651  -0.414  -0.414  -0.414  -0.651  -0.651  -0.651
186   V        -0.651  -0.651  -0.651  -0.651  -0.651  -0.651  -0.651  -0.651  -0.651
187   R        -0.651  -0.651  -0.651  -0.443  -0.443  -0.443  -0.651  -0.651  -0.651
188   F        -0.651  -0.651  -0.651  -0.853  -0.853  -0.853  -0.651  -0.651  -0.651
189   E        -0.651  -0.651  -0.651  -0.458  -0.458  -0.458  -0.651  -0.651  -0.651
* 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/P46998
Output conservation file - output/P46998
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
