1     M         0.867   0.869   0.879   0.947   0.946   0.961   0.893   0.894   0.905
2     A        -0.682  -0.659  -0.738  -0.639  -0.601  -0.742  -0.787  -0.751  -0.862
3     S        -1.807  -1.797  -1.734  -1.760  -1.739  -1.640  -1.627  -1.612  -1.515
4     R        -1.807  -1.797  -1.734  -1.860  -1.851  -1.736  -1.627  -1.612  -1.515
5     V        -0.820  -0.816  -0.770  -0.643  -0.637  -0.567  -0.997  -0.989  -0.910
6     D        -0.820  -0.816  -0.770  -1.007  -0.999  -0.915  -0.997  -0.989  -0.910
7     E        -0.820  -0.816  -0.770  -1.007  -0.999  -0.915  -0.997  -0.989  -0.910
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    T        -1.807  -1.797  -1.734  -1.688  -1.672  -1.570  -1.627  -1.612  -1.515
11    T        -0.682  -0.659  -0.738  -0.576  -0.542  -0.660  -0.787  -0.751  -0.862
12    V        -1.807  -1.797  -1.734  -1.501  -1.477  -1.391  -1.627  -1.612  -1.515
13    P         0.867   0.869   0.879   0.888   0.891   0.905   0.893   0.894   0.905
14    S        -0.682  -0.725  -0.749  -0.861  -0.927  -0.961  -0.787  -0.849  -0.879
15    Y         0.867   0.869   0.879   0.966   0.968   0.980   0.893   0.894   0.905
16    Y         0.867   0.869   0.879   0.966   0.968   0.980   0.893   0.894   0.905
17    Y         0.867   0.869   0.879   0.966   0.968   0.980   0.893   0.894   0.905
18    Y         0.867   0.869   0.879   0.966   0.968   0.980   0.893   0.894   0.905
19    V         0.867   0.869   0.879   0.956   0.957   0.971   0.893   0.894   0.905
20    D        -0.682  -0.659  -0.738  -0.861  -0.824  -0.936  -0.787  -0.751  -0.862
21    P         0.867   0.869   0.879   0.888   0.891   0.905   0.893   0.894   0.905
22    E        -0.682  -0.725  -0.749  -0.776  -0.856  -0.910  -0.787  -0.849  -0.879
23    T        -1.807  -1.797  -1.734  -1.670  -1.659  -1.553  -1.627  -1.612  -1.515
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    T        -1.807  -1.797  -1.734  -1.628  -1.614  -1.513  -1.627  -1.612  -1.515
26    Y         0.867   0.869   0.879   0.966   0.968   0.980   0.893   0.894   0.905
27    T        -1.807  -1.797  -1.734  -1.754  -1.739  -1.634  -1.627  -1.612  -1.515
28    Y        -1.807  -1.797  -1.734  -1.767  -1.760  -1.646  -1.627  -1.612  -1.515
29    Q         0.867   0.869   0.879   0.818   0.826   0.838   0.893   0.894   0.905
30    Q         0.867   0.869   0.879   0.818   0.826   0.838   0.893   0.894   0.905
31    P         0.867   0.869   0.879   0.888   0.891   0.905   0.893   0.894   0.905
32    N         0.867   0.869   0.879   0.808   0.813   0.828   0.893   0.894   0.905
33    P         0.867   0.869   0.879   0.888   0.891   0.905   0.893   0.894   0.905
34    L        -1.807  -1.797  -1.734  -1.646  -1.628  -1.530  -1.627  -1.612  -1.515
35    Q        -1.807  -1.797  -1.734  -1.899  -1.888  -1.773  -1.627  -1.612  -1.515
36    D         0.867   0.869   0.879   0.687   0.689   0.712   0.893   0.894   0.905
37    L         0.867   0.869   0.879   0.858   0.861   0.876   0.893   0.894   0.905
38    I         0.867   0.869   0.879   0.995   0.997   1.008   0.893   0.894   0.905
39    S        -0.682  -0.645  -0.738  -0.711  -0.645  -0.830  -0.787  -0.729  -0.862
40    V        -0.682  -0.725  -0.749  -0.546  -0.614  -0.652  -0.787  -0.849  -0.879
41    Y         0.867   0.869   0.879   0.966   0.968   0.980   0.893   0.894   0.905
42    G        -0.682  -0.659  -0.738  -0.524  -0.493  -0.594  -0.787  -0.751  -0.862
43    L         0.867   0.869   0.879   0.858   0.861   0.876   0.893   0.894   0.905
44    D        -0.682  -0.725  -0.749  -0.861  -0.929  -0.952  -0.787  -0.849  -0.879
45    D        -0.682  -0.725  -0.749  -0.861  -0.929  -0.952  -0.787  -0.849  -0.879
46    I        -0.682  -0.725  -0.749  -0.528  -0.599  -0.645  -0.787  -0.849  -0.879
47    S        -0.682  -0.725  -0.749  -0.804  -0.865  -0.887  -0.787  -0.849  -0.879
48    R         0.867   0.869   0.879   0.858   0.862   0.876   0.893   0.894   0.905
49    Q         0.867   0.869   0.879   0.818   0.826   0.838   0.893   0.894   0.905
50    V         0.867   0.869   0.879   0.956   0.957   0.971   0.893   0.894   0.905
51    A         0.867   0.869   0.879   0.927   0.929   0.943   0.893   0.894   0.905
52    R         0.867   0.869   0.879   0.858   0.862   0.876   0.893   0.894   0.905
53    T         0.867   0.869   0.879   0.917   0.917   0.933   0.893   0.894   0.905
54    N         0.867   0.869   0.879   0.808   0.813   0.828   0.893   0.894   0.905
55    L        -1.807  -1.797  -1.734  -1.724  -1.704  -1.605  -1.627  -1.612  -1.515
56    D         0.867   0.869   0.879   0.687   0.689   0.712   0.893   0.894   0.905
57    G         0.867   0.869   0.879   0.917   0.916   0.933   0.893   0.894   0.905
58    T         0.867   0.869   0.879   0.917   0.917   0.933   0.893   0.894   0.905
59    K         0.867   0.869   0.879   0.848   0.847   0.867   0.893   0.894   0.905
60    A         0.867   0.869   0.879   0.927   0.929   0.943   0.893   0.894   0.905
61    V         0.867   0.869   0.879   0.956   0.957   0.971   0.893   0.894   0.905
62    K         0.867   0.869   0.879   0.848   0.847   0.867   0.893   0.894   0.905
63    L         0.867   0.869   0.879   0.858   0.861   0.876   0.893   0.894   0.905
64    R         0.867   0.869   0.879   0.858   0.862   0.876   0.893   0.894   0.905
65    K         0.867   0.869   0.879   0.848   0.847   0.867   0.893   0.894   0.905
66    S         0.867   0.869   0.879   0.707   0.712   0.731   0.893   0.894   0.905
67    Y         0.867   0.869   0.879   0.966   0.968   0.980   0.893   0.894   0.905
68    K         0.867   0.869   0.879   0.848   0.847   0.867   0.893   0.894   0.905
69    N         0.867   0.869   0.879   0.808   0.813   0.828   0.893   0.894   0.905
70    Q         0.867   0.869   0.879   0.818   0.826   0.838   0.893   0.894   0.905
71    I         0.867   0.869   0.879   0.995   0.997   1.008   0.893   0.894   0.905
72    A        -1.807  -1.797  -1.734  -1.706  -1.693  -1.587  -1.627  -1.612  -1.515
73    D         0.867   0.869   0.879   0.687   0.689   0.712   0.893   0.894   0.905
74    L         0.867   0.869   0.879   0.858   0.861   0.876   0.893   0.894   0.905
75    S         0.867   0.869   0.879   0.707   0.712   0.731   0.893   0.894   0.905
76    G         0.867   0.869   0.879   0.917   0.916   0.933   0.893   0.894   0.905
77    K        -0.682  -0.725  -0.749  -0.707  -0.780  -0.819  -0.787  -0.849  -0.879
78    F         0.867   0.869   0.879   1.005   1.008   1.017   0.893   0.894   0.905
79    S        -0.682  -0.725  -0.749  -0.771  -0.829  -0.844  -0.787  -0.849  -0.879
80    T        -0.682  -0.659  -0.738  -0.711  -0.671  -0.830  -0.787  -0.751  -0.862
81    I         0.867   0.869   0.879   0.995   0.997   1.008   0.893   0.894   0.905
82    P         0.867   0.869   0.879   0.888   0.891   0.905   0.893   0.894   0.905
83    T        -1.807  -1.797  -1.734  -1.848  -1.839  -1.724  -1.627  -1.612  -1.515
84    R         0.867   0.869   0.879   0.858   0.862   0.876   0.893   0.894   0.905
85    E         0.867   0.869   0.879   0.848   0.848   0.867   0.893   0.894   0.905
86    N         0.867   0.869   0.879   0.808   0.813   0.828   0.893   0.894   0.905
87    G        -0.682  -0.659  -0.738  -0.643  -0.607  -0.744  -0.787  -0.751  -0.862
88    K         0.867   0.869   0.879   0.848   0.847   0.867   0.893   0.894   0.905
89    G         0.867   0.869   0.879   0.917   0.916   0.933   0.893   0.894   0.905
90    G         0.867   0.869   0.879   0.917   0.916   0.933   0.893   0.894   0.905
91    Q        -0.682  -0.645  -0.738  -0.725  -0.662  -0.823  -0.787  -0.729  -0.862
92    I         0.867   0.869   0.879   0.995   0.997   1.008   0.893   0.894   0.905
93    A        -0.682  -0.725  -0.749  -0.702  -0.782  -0.846  -0.787  -0.849  -0.879
94    H        -0.682  -0.725  -0.749  -0.532  -0.619  -0.703  -0.787  -0.849  -0.879
95    I        -0.682  -0.725  -0.749  -0.528  -0.599  -0.645  -0.787  -0.849  -0.879
96    L        -0.682  -0.725  -0.749  -0.634  -0.698  -0.728  -0.787  -0.849  -0.879
97    F         0.867   0.869   0.879   1.005   1.008   1.017   0.893   0.894   0.905
98    Q         0.867   0.869   0.879   0.818   0.826   0.838   0.893   0.894   0.905
99    N         0.867   0.869   0.879   0.808   0.813   0.828   0.893   0.894   0.905
100   N         0.867   0.869   0.879   0.808   0.813   0.828   0.893   0.894   0.905
101   P         0.867   0.869   0.879   0.888   0.891   0.905   0.893   0.894   0.905
102   D         0.867   0.869   0.879   0.687   0.689   0.712   0.893   0.894   0.905
103   M         0.867   0.869   0.879   0.947   0.946   0.961   0.893   0.894   0.905
104   M         0.867   0.869   0.879   0.947   0.946   0.961   0.893   0.894   0.905
105   I        -0.682  -0.645  -0.738  -0.680  -0.621  -0.751  -0.787  -0.729  -0.862
106   Q         0.867   0.869   0.879   0.818   0.826   0.838   0.893   0.894   0.905
107   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   P        -1.807  -1.797  -1.734  -1.640  -1.623  -1.524  -1.627  -1.612  -1.515
109   Q        -1.807  -1.797  -1.734  -1.628  -1.615  -1.513  -1.627  -1.612  -1.515
110   Q        -1.807  -1.797  -1.734  -1.785  -1.762  -1.664  -1.627  -1.612  -1.515
111   G        -1.807  -1.797  -1.734  -1.754  -1.733  -1.634  -1.627  -1.612  -1.515
112   Q        -1.807  -1.797  -1.734  -1.773  -1.753  -1.652  -1.627  -1.612  -1.515
113   N        -1.807  -1.797  -1.734  -1.860  -1.835  -1.736  -1.627  -1.612  -1.515
114   M         0.867   0.869   0.879   0.947   0.946   0.961   0.893   0.894   0.905
115   S        -0.682  -0.659  -0.738  -0.809  -0.771  -0.878  -0.787  -0.751  -0.862
116   E        -0.682  -0.659  -0.738  -0.785  -0.746  -0.899  -0.787  -0.751  -0.862
117   Q        -0.682  -0.645  -0.738  -0.725  -0.662  -0.823  -0.787  -0.729  -0.862
118   Q        -0.682  -0.725  -0.749  -0.739  -0.806  -0.848  -0.787  -0.849  -0.879
119   W        -0.682  -0.725  -0.749  -0.369  -0.443  -0.507  -0.787  -0.849  -0.879
120   R         0.867   0.869   0.879   0.858   0.862   0.876   0.893   0.894   0.905
121   E        -0.682  -0.725  -0.749  -0.785  -0.867  -0.922  -0.787  -0.849  -0.879
122   Q        -0.682  -0.645  -0.738  -0.652  -0.586  -0.759  -0.787  -0.729  -0.862
123   L        -0.682  -0.725  -0.749  -0.657  -0.724  -0.757  -0.787  -0.849  -0.879
124   R        -0.682  -0.645  -0.738  -0.617  -0.556  -0.720  -0.787  -0.729  -0.862
125   N        -0.682  -0.725  -0.749  -0.748  -0.818  -0.856  -0.787  -0.849  -0.879
126   R        -0.682  -0.659  -0.738  -0.652  -0.615  -0.734  -0.787  -0.751  -0.862
127   D         0.867   0.869   0.879   0.687   0.689   0.712   0.893   0.894   0.905
128   I        -1.807  -1.797  -1.734  -1.599  -1.587  -1.484  -1.627  -1.612  -1.515
129   A        -1.807  -1.797  -1.734  -1.773  -1.753  -1.652  -1.627  -1.612  -1.515
130   L         0.867   0.869   0.879   0.858   0.861   0.876   0.893   0.894   0.905
131   F         0.867   0.869   0.879   1.005   1.008   1.017   0.893   0.894   0.905
132   Q        -0.682  -0.725  -0.749  -0.739  -0.806  -0.848  -0.787  -0.849  -0.879
133   P        -0.682  -0.659  -0.738  -0.639  -0.600  -0.728  -0.787  -0.751  -0.862
134   P         0.867   0.869   0.879   0.888   0.891   0.905   0.893   0.894   0.905
135   N        -0.682  -0.725  -0.749  -0.762  -0.829  -0.875  -0.787  -0.849  -0.879
136   F        -0.682  -0.645  -0.738  -0.550  -0.494  -0.637  -0.787  -0.729  -0.862
137   D         0.867   0.869   0.879   0.687   0.689   0.712   0.893   0.894   0.905
138   W         0.867   0.869   0.879   1.167   1.169   1.173   0.893   0.894   0.905
139   D        -0.682  -0.659  -0.738  -0.861  -0.824  -0.936  -0.787  -0.751  -0.862
140   L        -1.807  -1.797  -1.734  -1.646  -1.629  -1.530  -1.627  -1.612  -1.515
141   C         0.867   0.869   0.879   1.186   1.187   1.191   0.893   0.894   0.905
142   S        -0.682  -0.659  -0.738  -0.856  -0.813  -0.937  -0.787  -0.751  -0.862
143   S        -0.682  -0.725  -0.749  -0.809  -0.872  -0.893  -0.787  -0.849  -0.879
144   V         0.867   0.869   0.879   0.956   0.957   0.971   0.893   0.894   0.905
145   L        -0.682  -0.725  -0.749  -0.634  -0.698  -0.728  -0.787  -0.849  -0.879
146   S        -0.682  -0.725  -0.749  -0.809  -0.872  -0.893  -0.787  -0.849  -0.879
147   Q         0.867   0.869   0.879   0.818   0.826   0.838   0.893   0.894   0.905
148   F        -0.682  -0.725  -0.749  -0.563  -0.636  -0.695  -0.787  -0.849  -0.879
149   E        -1.807  -1.797  -1.734  -1.816  -1.794  -1.693  -1.627  -1.612  -1.515
150   R        -0.682  -0.725  -0.749  -0.702  -0.774  -0.817  -0.787  -0.849  -0.879
151   S         0.867   0.869   0.879   0.707   0.712   0.731   0.893   0.894   0.905
152   Y        -0.682  -0.725  -0.749  -0.480  -0.542  -0.571  -0.787  -0.849  -0.879
153   P         0.867   0.869   0.879   0.888   0.891   0.905   0.893   0.894   0.905
154   S        -0.682  -0.659  -0.738  -0.809  -0.771  -0.878  -0.787  -0.751  -0.862
155   E         0.867   0.869   0.879   0.848   0.848   0.867   0.893   0.894   0.905
156   F         0.867   0.869   0.879   1.005   1.008   1.017   0.893   0.894   0.905
157   A        -1.807  -1.797  -1.734  -1.748  -1.733  -1.628  -1.627  -1.612  -1.515
158   N         0.867   0.869   0.879   0.808   0.813   0.828   0.893   0.894   0.905
159   Q        -0.820  -0.816  -0.770  -1.123  -1.115  -1.027  -0.997  -0.989  -0.910
160   N        -0.820  -0.816  -0.770  -0.982  -0.975  -0.892  -0.997  -0.989  -0.910
161   Q        -0.820  -0.816  -0.770  -1.068  -1.061  -0.974  -0.997  -0.989  -0.910
162   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   A        -0.820  -0.816  -0.770  -1.038  -1.031  -0.946  -0.997  -0.989  -0.910
167   P        -0.820  -0.816  -0.770  -0.944  -0.937  -0.855  -0.997  -0.989  -0.910
168   F         0.867   0.869   0.879   1.005   1.008   1.017   0.893   0.894   0.905
169   D        -0.682  -0.659  -0.738  -0.730  -0.698  -0.772  -0.787  -0.751  -0.862
170   I        -0.682  -0.645  -0.738  -0.546  -0.489  -0.635  -0.787  -0.729  -0.862
171   D         0.867   0.869   0.879   0.687   0.689   0.712   0.893   0.894   0.905
172   D         0.867   0.869   0.879   0.687   0.689   0.712   0.893   0.894   0.905
173   L         0.867   0.869   0.879   0.858   0.861   0.876   0.893   0.894   0.905
174   A         0.867   0.869   0.879   0.927   0.929   0.943   0.893   0.894   0.905
175   F         0.867   0.869   0.879   1.005   1.008   1.017   0.893   0.894   0.905
176   D         0.867   0.869   0.879   0.687   0.689   0.712   0.893   0.894   0.905
177   L         0.867   0.869   0.879   0.858   0.861   0.876   0.893   0.894   0.905
178   D        -0.682  -0.725  -0.749  -0.880  -0.947  -0.977  -0.787  -0.849  -0.879
179   G         0.867   0.869   0.879   0.917   0.916   0.933   0.893   0.894   0.905
180   T         0.867   0.869   0.879   0.917   0.917   0.933   0.893   0.894   0.905
181   G         0.867   0.869   0.879   0.917   0.916   0.933   0.893   0.894   0.905
182   K         0.867   0.869   0.879   0.898   0.901   0.915   0.893   0.894   0.905
183   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   N        -1.807  -1.797  -1.734  -1.848  -1.821  -1.724  -1.627  -1.612  -1.515
192   N        -0.682  -0.725  -0.749  -0.748  -0.818  -0.856  -0.787  -0.849  -0.879
193   S        -1.807  -1.797  -1.734  -1.773  -1.749  -1.652  -1.627  -1.612  -1.515
194   K         0.867   0.869   0.879   0.848   0.847   0.867   0.893   0.894   0.905
195   K         0.867   0.869   0.879   0.848   0.847   0.867   0.893   0.894   0.905
196   R         0.867   0.869   0.879   0.858   0.862   0.876   0.893   0.894   0.905
197   K         0.867   0.869   0.879   0.848   0.847   0.867   0.893   0.894   0.905
198   N        -0.682  -0.725  -0.749  -0.693  -0.756  -0.784  -0.787  -0.849  -0.879
199   K        -0.682  -0.659  -0.738  -0.707  -0.671  -0.800  -0.787  -0.751  -0.862
200   S         0.867   0.869   0.879   0.707   0.712   0.731   0.893   0.894   0.905
201   S        -0.682  -0.645  -0.738  -0.813  -0.744  -0.920  -0.787  -0.729  -0.862
202   G         0.867   0.869   0.879   0.917   0.916   0.933   0.893   0.894   0.905
203   S         0.867   0.869   0.879   0.707   0.712   0.731   0.893   0.894   0.905
204   S         0.867   0.869   0.879   0.707   0.712   0.731   0.893   0.894   0.905
205   M         0.867   0.869   0.879   0.947   0.946   0.961   0.893   0.894   0.905
206   A         0.867   0.869   0.879   0.927   0.929   0.943   0.893   0.894   0.905
207   T        -0.682  -0.725  -0.749  -0.711  -0.792  -0.854  -0.787  -0.849  -0.879
208   P         0.867   0.869   0.879   0.888   0.891   0.905   0.893   0.894   0.905
209   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
210   H        -0.682  -0.645  -0.738  -0.621  -0.566  -0.678  -0.787  -0.729  -0.862
211   S        -0.682  -0.725  -0.749  -0.809  -0.872  -0.893  -0.787  -0.849  -0.879
212   D        -0.682  -0.645  -0.738  -0.785  -0.721  -0.899  -0.787  -0.729  -0.862
213   S        -1.807  -1.797  -1.734  -1.798  -1.777  -1.675  -1.627  -1.612  -1.515
214   H        -0.682  -0.645  -0.738  -0.612  -0.554  -0.670  -0.787  -0.729  -0.862
215   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
216   E        -0.682  -0.645  -0.738  -0.861  -0.802  -0.936  -0.787  -0.729  -0.862
217   D         0.867   0.869   0.879   0.687   0.689   0.712   0.893   0.894   0.905
218   M        -0.682  -0.659  -0.738  -0.572  -0.539  -0.664  -0.787  -0.751  -0.862
219   K         0.867   0.869   0.879   0.848   0.847   0.867   0.893   0.894   0.905
220   R         0.867   0.869   0.879   0.858   0.862   0.876   0.893   0.894   0.905
221   R         0.867   0.869   0.879   0.858   0.862   0.876   0.893   0.894   0.905
222   R         0.867   0.869   0.879   0.858   0.862   0.876   0.893   0.894   0.905
223   L         0.867   0.869   0.879   0.858   0.861   0.876   0.893   0.894   0.905
224   E         0.867   0.869   0.879   0.848   0.848   0.867   0.893   0.894   0.905
* 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/P25046
Output conservation file - output/P25046
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
