1     M         1.472   1.472   1.472   1.801   1.797   1.801   1.472   1.472   1.472
2     Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     E         1.472   1.472   1.472   1.524   1.509   1.524   1.472   1.472   1.472
5     E        -0.675  -0.675  -0.675  -0.624  -0.623  -0.624  -0.675  -0.675  -0.675
6     R        -0.675  -0.675  -0.675  -0.849  -0.857  -0.849  -0.675  -0.675  -0.675
7     L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
8     Q        -0.675  -0.675  -0.675  -0.692  -0.694  -0.692  -0.675  -0.675  -0.675
9     Q        -0.675  -0.675  -0.675  -0.590  -0.571  -0.590  -0.675  -0.675  -0.675
10    L        -0.675  -0.675  -0.675  -1.278  -1.303  -1.278  -0.675  -0.675  -0.675
11    V        -0.675  -0.675  -0.675  -1.278  -1.303  -1.278  -0.675  -0.675  -0.675
12    E        -0.675  -0.675  -0.675  -0.624  -0.623  -0.624  -0.675  -0.675  -0.675
13    S        -0.675  -0.675  -0.675  -0.796  -0.784  -0.796  -0.675  -0.675  -0.675
14    D        -0.675  -0.675  -0.675  -0.474  -0.468  -0.474  -0.675  -0.675  -0.675
15    W        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    P        -0.675  -0.675  -0.675  -0.360  -0.350  -0.360  -0.675  -0.675  -0.675
23    N        -0.675  -0.675  -0.675  -0.441  -0.434  -0.441  -0.675  -0.675  -0.675
24    V         1.472   1.472   1.472   1.357   1.361   1.357   1.472   1.472   1.472
25    L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
26    V         1.472   1.472   1.472   1.357   1.361   1.357   1.472   1.472   1.472
27    I         1.472   1.472   1.472   1.687   1.702   1.687   1.472   1.472   1.472
28    V        -0.675  -0.675  -0.675  -0.658  -0.659  -0.658  -0.675  -0.675  -0.675
29    L        -0.675  -0.675  -0.675  -1.278  -1.303  -1.278  -0.675  -0.675  -0.675
30    G         1.472   1.472   1.472   1.687   1.678   1.687   1.472   1.472   1.472
31    D        -0.675  -0.675  -0.675  -0.744  -0.730  -0.744  -0.675  -0.675  -0.675
32    T        -0.675  -0.675  -0.675  -0.474  -0.468  -0.474  -0.675  -0.675  -0.675
33    A         1.472   1.472   1.472   1.778   1.773   1.778   1.472   1.472   1.472
34    R         1.472   1.472   1.472   1.524   1.509   1.524   1.472   1.472   1.472
35    K        -0.675  -0.675  -0.675  -0.658  -0.623  -0.658  -0.675  -0.675  -0.675
36    Y        -0.675  -0.675  -0.675  -0.424  -0.384  -0.424  -0.675  -0.675  -0.675
37    V        -0.675  -0.675  -0.675  -0.624  -0.623  -0.624  -0.675  -0.675  -0.675
38    E         1.472   1.472   1.472   1.524   1.509   1.524   1.472   1.472   1.472
39    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    G        -0.675  -0.675  -0.675  -0.573  -0.571  -0.573  -0.675  -0.675  -0.675
41    G        -0.675  -0.675  -0.675  -0.507  -0.502  -0.507  -0.675  -0.675  -0.675
42    L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
43    K        -0.675  -0.675  -0.675  -0.590  -0.588  -0.590  -0.675  -0.675  -0.675
44    E         1.472   1.472   1.472   1.524   1.509   1.524   1.472   1.472   1.472
45    H        -0.675  -0.675  -0.675  -0.312  -0.317  -0.312  -0.675  -0.675  -0.675
46    V        -0.675  -0.675  -0.675  -0.709  -0.694  -0.709  -0.675  -0.675  -0.675
47    T         1.472   1.472   1.472   1.687   1.678   1.687   1.472   1.472   1.472
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    T        -0.675  -0.675  -0.675  -0.392  -0.400  -0.392  -0.675  -0.675  -0.675
51    N         1.472   1.472   1.472   1.733   1.726   1.733   1.472   1.472   1.472
52    T        -0.675  -0.675  -0.675  -0.675  -0.659  -0.675  -0.675  -0.675  -0.675
53    V        -0.675  -0.675  -0.675  -0.727  -0.712  -0.727  -0.675  -0.675  -0.675
54    A        -0.675  -0.675  -0.675  -0.441  -0.434  -0.441  -0.675  -0.675  -0.675
55    G        -0.675  -0.675  -0.675  -0.507  -0.502  -0.507  -0.675  -0.675  -0.675
56    H        -0.675  -0.675  -0.675  -0.344  -0.334  -0.344  -0.675  -0.675  -0.675
57    V         1.472   1.472   1.472   1.357   1.361   1.357   1.472   1.472   1.472
58    A        -0.675  -0.675  -0.675  -0.540  -0.554  -0.540  -0.675  -0.675  -0.675
59    S        -0.675  -0.675  -0.675  -0.675  -0.659  -0.675  -0.675  -0.675  -0.675
60    R         1.472   1.472   1.472   1.524   1.509   1.524   1.472   1.472   1.472
61    E        -0.675  -0.675  -0.675  -0.796  -0.784  -0.796  -0.675  -0.675  -0.675
62    R        -0.675  -0.675  -0.675  -0.573  -0.588  -0.573  -0.675  -0.675  -0.675
63    V         1.472   1.472   1.472   1.357   1.361   1.357   1.472   1.472   1.472
64    S        -0.675  -0.675  -0.675  -0.796  -0.784  -0.796  -0.675  -0.675  -0.675
65    V        -0.675  -0.675  -0.675  -0.727  -0.712  -0.727  -0.675  -0.675  -0.675
66    V        -0.675  -0.675  -0.675  -1.278  -1.303  -1.278  -0.675  -0.675  -0.675
67    F         1.472   1.472   1.472   1.823   1.820   1.823   1.472   1.472   1.472
68    L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
69    G        -0.675  -0.675  -0.675  -0.507  -0.502  -0.507  -0.675  -0.675  -0.675
70    R        -0.675  -0.675  -0.675  -0.590  -0.588  -0.590  -0.675  -0.675  -0.675
71    V        -0.675  -0.675  -0.675  -1.278  -1.303  -1.278  -0.675  -0.675  -0.675
72    K        -0.675  -0.675  -0.675  -0.556  -0.536  -0.556  -0.675  -0.675  -0.675
73    Y         1.472   1.472   1.472   1.640   1.702   1.640   1.472   1.472   1.472
74    L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
75    Y         1.472   1.472   1.472   1.640   1.702   1.640   1.472   1.472   1.472
76    M         1.472   1.472   1.472   1.801   1.797   1.801   1.472   1.472   1.472
77    Y         1.472   1.472   1.472   1.640   1.702   1.640   1.472   1.472   1.472
78    L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
79    T         1.472   1.472   1.472   1.687   1.678   1.687   1.472   1.472   1.472
80    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    R        -0.675  -0.675  -0.675  -0.727  -0.748  -0.727  -0.675  -0.675  -0.675
85    M        -0.675  -0.675  -0.675  -0.921  -0.950  -0.921  -0.675  -0.675  -0.675
86    Q         1.472   1.472   1.472   1.571   1.582   1.571   1.472   1.472   1.472
87    A        -0.675  -0.675  -0.675  -0.392  -0.400  -0.392  -0.675  -0.675  -0.675
88    Q        -0.675  -0.675  -0.675  -0.556  -0.536  -0.556  -0.675  -0.675  -0.675
89    A        -0.675  -0.675  -0.675  -0.424  -0.434  -0.424  -0.675  -0.675  -0.675
90    N         1.472   1.472   1.472   1.733   1.726   1.733   1.472   1.472   1.472
91    G        -0.675  -0.675  -0.675  -0.490  -0.502  -0.490  -0.675  -0.675  -0.675
92    P        -0.675  -0.675  -0.675  -0.556  -0.536  -0.556  -0.675  -0.675  -0.675
93    Q        -0.675  -0.675  -0.675  -0.490  -0.485  -0.490  -0.675  -0.675  -0.675
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    Y         1.472   1.472   1.472   1.640   1.702   1.640   1.472   1.472   1.472
96    S        -0.675  -0.675  -0.675  -0.796  -0.784  -0.796  -0.675  -0.675  -0.675
97    N        -0.675  -0.675  -0.675  -0.573  -0.588  -0.573  -0.675  -0.675  -0.675
98    V        -0.675  -0.675  -0.675  -0.727  -0.712  -0.727  -0.675  -0.675  -0.675
99    L        -0.675  -0.675  -0.675  -1.012  -1.026  -1.012  -0.675  -0.675  -0.675
100   V        -0.675  -0.675  -0.675  -0.727  -0.712  -0.727  -0.675  -0.675  -0.675
101   Y         1.472   1.472   1.472   1.640   1.702   1.640   1.472   1.472   1.472
102   G         1.472   1.472   1.472   1.687   1.678   1.687   1.472   1.472   1.472
103   L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
104   W        -0.675  -0.675  -0.675  -0.441  -0.434  -0.441  -0.675  -0.675  -0.675
105   D        -0.675  -0.675  -0.675  -0.692  -0.659  -0.692  -0.675  -0.675  -0.675
106   L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
107   T        -0.675  -0.675  -0.675  -1.012  -1.045  -1.012  -0.675  -0.675  -0.675
108   A        -0.675  -0.675  -0.675  -0.344  -0.350  -0.344  -0.675  -0.675  -0.675
109   T         1.472   1.472   1.472   1.687   1.678   1.687   1.472   1.472   1.472
110   Q        -0.675  -0.675  -0.675  -0.556  -0.536  -0.556  -0.675  -0.675  -0.675
111   D        -0.675  -0.675  -0.675  -0.624  -0.623  -0.624  -0.675  -0.675  -0.675
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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
125   G        -0.675  -0.675  -0.675  -0.675  -0.659  -0.675  -0.675  -0.675  -0.675
126   P        -0.675  -0.675  -0.675  -0.376  -0.367  -0.376  -0.675  -0.675  -0.675
127   Q        -0.675  -0.675  -0.675  -0.761  -0.730  -0.761  -0.675  -0.675  -0.675
128   Q         1.472   1.472   1.472   1.571   1.582   1.571   1.472   1.472   1.472
129   L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
130   R         1.472   1.472   1.472   1.524   1.509   1.524   1.472   1.472   1.472
131   L        -0.675  -0.675  -0.675  -0.849  -0.876  -0.849  -0.675  -0.675  -0.675
132   L        -0.675  -0.675  -0.675  -0.796  -0.821  -0.796  -0.675  -0.675  -0.675
133   S        -0.675  -0.675  -0.675  -0.641  -0.623  -0.641  -0.675  -0.675  -0.675
134   L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
135   V        -0.675  -0.675  -0.675  -0.727  -0.712  -0.727  -0.675  -0.675  -0.675
136   L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
137   R        -0.675  -0.675  -0.675  -0.457  -0.468  -0.457  -0.675  -0.675  -0.675
138   Q        -0.675  -0.675  -0.675  -0.573  -0.571  -0.573  -0.675  -0.675  -0.675
139   C        -0.675  -0.675  -0.675  -0.474  -0.451  -0.474  -0.675  -0.675  -0.675
140   L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
141   S        -0.675  -0.675  -0.675  -0.796  -0.784  -0.796  -0.675  -0.675  -0.675
142   L         1.472   1.472   1.472   0.959   0.923   0.959   1.472   1.472   1.472
143   P        -0.675  -0.675  -0.675  -0.490  -0.502  -0.490  -0.675  -0.675  -0.675
144   S        -0.675  -0.675  -0.675  -0.641  -0.623  -0.641  -0.675  -0.675  -0.675
145   K        -0.675  -0.675  -0.675  -0.556  -0.536  -0.556  -0.675  -0.675  -0.675
146   V        -0.675  -0.675  -0.675  -0.761  -0.712  -0.761  -0.675  -0.675  -0.675
147   E        -0.675  -0.675  -0.675  -0.540  -0.554  -0.540  -0.675  -0.675  -0.675
148   F        -0.675  -0.675  -0.675  -0.624  -0.623  -0.624  -0.675  -0.675  -0.675
149   Y        -0.675  -0.675  -0.675  -0.641  -0.606  -0.641  -0.675  -0.675  -0.675
150   P        -0.675  -0.675  -0.675  -0.376  -0.367  -0.376  -0.675  -0.675  -0.675
151   E        -0.675  -0.675  -0.675  -0.727  -0.748  -0.727  -0.675  -0.675  -0.675
152   P        -0.675  -0.675  -0.675  -0.296  -0.301  -0.296  -0.675  -0.675  -0.675
153   P        -0.675  -0.675  -0.675  -0.607  -0.606  -0.607  -0.675  -0.675  -0.675
154   S         1.472   1.472   1.472   1.429   1.460   1.429   1.472   1.472   1.472
155   S        -0.675  -0.675  -0.675  -0.607  -0.588  -0.607  -0.675  -0.675  -0.675
156   S        -0.675  -0.675  -0.675  -0.675  -0.659  -0.675  -0.675  -0.675  -0.675
157   V        -0.675  -0.675  -0.675  -0.744  -0.730  -0.744  -0.675  -0.675  -0.675
158   P        -0.675  -0.675  -0.675  -0.885  -0.913  -0.885  -0.675  -0.675  -0.675
159   A        -0.675  -0.675  -0.675  -0.424  -0.434  -0.424  -0.675  -0.675  -0.675
160   R        -0.675  -0.675  -0.675  -0.523  -0.536  -0.523  -0.675  -0.675  -0.675
161   L        -0.675  -0.675  -0.675  -0.921  -0.950  -0.921  -0.675  -0.675  -0.675
162   L        -0.675  -0.675  -0.675  -1.220  -1.222  -1.220  -0.675  -0.675  -0.675
163   R        -0.675  -0.675  -0.675  -0.692  -0.694  -0.692  -0.675  -0.675  -0.675
164   F        -0.675  -0.675  -0.675  -0.392  -0.400  -0.392  -0.675  -0.675  -0.675
165   W         1.472   1.472   1.472   1.913   1.936   1.913   1.472   1.472   1.472
166   D        -0.675  -0.675  -0.675  -0.490  -0.468  -0.490  -0.675  -0.675  -0.675
167   H        -0.675  -0.675  -0.675  -0.312  -0.317  -0.312  -0.675  -0.675  -0.675
168   I        -0.675  -0.675  -0.675  -1.012  -1.026  -1.012  -0.675  -0.675  -0.675
169   I        -0.675  -0.675  -0.675  -0.490  -0.485  -0.490  -0.675  -0.675  -0.675
170   R        -0.675  -0.675  -0.675  -0.727  -0.748  -0.727  -0.675  -0.675  -0.675
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     *
* 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/P38751
Output conservation file - output/P38751
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
