1     M         1.449   1.449   1.449   1.869   1.869   1.869   1.449   1.449   1.449
2     S        -0.686  -0.686  -0.686  -0.595  -0.595  -0.595  -0.686  -0.686  -0.686
3     V        -0.686  -0.686  -0.686  -0.052  -0.052  -0.052  -0.686  -0.686  -0.686
4     S        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
5     K        -0.686  -0.686  -0.686   0.107   0.107   0.107  -0.686  -0.686  -0.686
6     I        -0.686  -0.686  -0.686  -0.096  -0.096  -0.096  -0.686  -0.686  -0.686
7     A        -0.686  -0.686  -0.686  -0.760  -0.760  -0.760  -0.686  -0.686  -0.686
8     F        -0.686  -0.686  -0.686  -0.052  -0.052  -0.052  -0.686  -0.686  -0.686
9     V        -0.686  -0.686  -0.686  -0.907  -0.907  -0.907  -0.686  -0.686  -0.686
10    L         1.449   1.449   1.449   1.424   1.424   1.424   1.449   1.449   1.449
11    S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    A        -0.686  -0.686  -0.686  -0.786  -0.786  -0.786  -0.686  -0.686  -0.686
14    I        -0.686  -0.686  -0.686  -0.117  -0.117  -0.117  -0.686  -0.686  -0.686
15    A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
16    S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
17    L         1.449   1.449   1.449   1.424   1.424   1.424   1.449   1.449   1.449
18    A        -0.686  -0.686  -0.686  -0.722  -0.722  -0.722  -0.686  -0.686  -0.686
19    V        -0.686  -0.686  -0.686  -0.722  -0.722  -0.722  -0.686  -0.686  -0.686
20    A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
21    D        -0.686  -0.686  -0.686   0.001   0.001   0.001  -0.686  -0.686  -0.686
22    T        -0.686  -0.686  -0.686  -0.760  -0.760  -0.760  -0.686  -0.686  -0.686
23    S        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
24    A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
25    A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
26    E        -0.686  -0.686  -0.686   0.001   0.001   0.001  -0.686  -0.686  -0.686
27    T        -0.686  -0.686  -0.686  -0.286  -0.286  -0.286  -0.686  -0.686  -0.686
28    A        -0.686  -0.686  -0.686  -0.473  -0.473  -0.473  -0.686  -0.686  -0.686
29    E        -0.686  -0.686  -0.686   0.096   0.096   0.096  -0.686  -0.686  -0.686
30    L         1.449   1.449   1.449   1.424   1.424   1.424   1.449   1.449   1.449
31    Q        -0.686  -0.686  -0.686  -0.063  -0.063  -0.063  -0.686  -0.686  -0.686
32    A         1.449   1.449   1.449   0.853   0.853   0.853   1.449   1.449   1.449
33    I        -0.686  -0.686  -0.686  -0.117  -0.117  -0.117  -0.686  -0.686  -0.686
34    I        -0.686  -0.686  -0.686  -0.063  -0.063  -0.063  -0.686  -0.686  -0.686
35    G         1.449   1.449   1.449   1.582   1.582   1.582   1.449   1.449   1.449
36    D         1.449   1.449   1.449   1.643   1.643   1.643   1.449   1.449   1.449
37    I        -0.686  -0.686  -0.686   0.117   0.117   0.117  -0.686  -0.686  -0.686
38    N        -0.686  -0.686  -0.686   0.189   0.189   0.189  -0.686  -0.686  -0.686
39    S        -0.686  -0.686  -0.686  -0.786  -0.786  -0.786  -0.686  -0.686  -0.686
40    H         1.449   1.449   1.449   1.898   1.898   1.898   1.449   1.449   1.449
41    L        -0.686  -0.686  -0.686  -0.139  -0.139  -0.139  -0.686  -0.686  -0.686
42    S        -0.686  -0.686  -0.686  -0.948  -0.948  -0.948  -0.686  -0.686  -0.686
43    D         1.449   1.449   1.449   1.643   1.643   1.643   1.449   1.449   1.449
44    Y         1.449   1.449   1.449   1.765   1.765   1.765   1.449   1.449   1.449
45    L        -0.686  -0.686  -0.686  -0.117  -0.117  -0.117  -0.686  -0.686  -0.686
46    G        -0.686  -0.686  -0.686  -0.031  -0.031  -0.031  -0.686  -0.686  -0.686
47    L        -0.686  -0.686  -0.686  -0.107  -0.107  -0.107  -0.686  -0.686  -0.686
48    E        -0.686  -0.686  -0.686   0.096   0.096   0.096  -0.686  -0.686  -0.686
49    T        -0.686  -0.686  -0.686  -0.760  -0.760  -0.760  -0.686  -0.686  -0.686
50    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    S        -0.686  -0.686  -0.686  -0.948  -0.948  -0.948  -0.686  -0.686  -0.686
53    G        -0.686  -0.686  -0.686  -0.658  -0.658  -0.658  -0.686  -0.686  -0.686
54    F        -0.686  -0.686  -0.686   0.107   0.107   0.107  -0.686  -0.686  -0.686
55    Q        -0.686  -0.686  -0.686   0.065   0.065   0.065  -0.686  -0.686  -0.686
56    I        -0.686  -0.686  -0.686  -0.063  -0.063  -0.063  -0.686  -0.686  -0.686
57    P         1.449   1.449   1.449   1.780   1.780   1.780   1.449   1.449   1.449
58    S        -0.686  -0.686  -0.686  -0.839  -0.839  -0.839  -0.686  -0.686  -0.686
59    D         1.449   1.449   1.449   1.643   1.643   1.643   1.449   1.449   1.449
60    V        -0.686  -0.686  -0.686  -0.308  -0.308  -0.308  -0.686  -0.686  -0.686
61    L        -0.686  -0.686  -0.686  -0.975  -0.975  -0.975  -0.686  -0.686  -0.686
62    S        -0.686  -0.686  -0.686  -0.948  -0.948  -0.948  -0.686  -0.686  -0.686
63    V        -0.686  -0.686  -0.686  -0.308  -0.308  -0.308  -0.686  -0.686  -0.686
64    Y        -0.686  -0.686  -0.686  -0.509  -0.509  -0.509  -0.686  -0.686  -0.686
65    Q        -0.686  -0.686  -0.686  -0.063  -0.063  -0.063  -0.686  -0.686  -0.686
66    Q        -0.686  -0.686  -0.686   0.127   0.127   0.127  -0.686  -0.686  -0.686
67    V         1.449   1.449   1.449   1.503   1.503   1.503   1.449   1.449   1.449
68    M        -0.686  -0.686  -0.686  -0.041  -0.041  -0.041  -0.686  -0.686  -0.686
69    T         1.449   1.449   1.449   1.456   1.456   1.456   1.449   1.449   1.449
70    Y         1.449   1.449   1.449   1.765   1.765   1.765   1.449   1.449   1.449
71    T         1.449   1.449   1.449   1.456   1.456   1.456   1.449   1.449   1.449
72    D         1.449   1.449   1.449   1.643   1.643   1.643   1.449   1.449   1.449
73    D         1.449   1.449   1.449   1.643   1.643   1.643   1.449   1.449   1.449
74    A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
75    Y         1.449   1.449   1.449   1.765   1.765   1.765   1.449   1.449   1.449
76    T         1.449   1.449   1.449   1.456   1.456   1.456   1.449   1.449   1.449
77    T         1.449   1.449   1.449   1.456   1.456   1.456   1.449   1.449   1.449
78    L         1.449   1.449   1.449   1.424   1.424   1.424   1.449   1.449   1.449
79    F        -0.686  -0.686  -0.686  -0.107  -0.107  -0.107  -0.686  -0.686  -0.686
80    S        -0.686  -0.686  -0.686  -0.633  -0.633  -0.633  -0.686  -0.686  -0.686
81    E        -0.686  -0.686  -0.686   0.001   0.001   0.001  -0.686  -0.686  -0.686
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    L         1.449   1.449   1.449   1.424   1.424   1.424   1.449   1.449   1.449
85    D        -0.686  -0.686  -0.686   0.075   0.075   0.075  -0.686  -0.686  -0.686
86    F        -0.686  -0.686  -0.686  -0.052  -0.052  -0.052  -0.686  -0.686  -0.686
87    D        -0.686  -0.686  -0.686  -0.786  -0.786  -0.786  -0.686  -0.686  -0.686
88    A        -0.686  -0.686  -0.686  -0.461  -0.461  -0.461  -0.686  -0.686  -0.686
89    I        -0.686  -0.686  -0.686  -0.117  -0.117  -0.117  -0.686  -0.686  -0.686
90    T        -0.686  -0.686  -0.686  -0.128  -0.128  -0.128  -0.686  -0.686  -0.686
91    K        -0.686  -0.686  -0.686  -0.534  -0.534  -0.534  -0.686  -0.686  -0.686
92    T        -0.686  -0.686  -0.686  -0.096  -0.096  -0.096  -0.686  -0.686  -0.686
93    I        -0.686  -0.686  -0.686  -0.509  -0.509  -0.509  -0.686  -0.686  -0.686
94    V        -0.686  -0.686  -0.686  -0.286  -0.286  -0.286  -0.686  -0.686  -0.686
95    K        -0.686  -0.686  -0.686  -0.709  -0.709  -0.709  -0.686  -0.686  -0.686
96    L         1.449   1.449   1.449   1.424   1.424   1.424   1.449   1.449   1.449
97    P         1.449   1.449   1.449   1.780   1.780   1.780   1.449   1.449   1.449
98    W         1.449   1.449   1.449   1.898   1.898   1.898   1.449   1.449   1.449
99    Y         1.449   1.449   1.449   1.765   1.765   1.765   1.449   1.449   1.449
100   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
101   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
105   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
109   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
117   A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
118   S        -0.686  -0.686  -0.686  -0.595  -0.595  -0.595  -0.686  -0.686  -0.686
119   S        -0.686  -0.686  -0.686  -0.683  -0.683  -0.683  -0.686  -0.686  -0.686
120   E        -0.686  -0.686  -0.686   0.117   0.117   0.117  -0.686  -0.686  -0.686
121   A         1.449   1.449   1.449   0.853   0.853   0.853   1.449   1.449   1.449
122   A        -0.686  -0.686  -0.686  -0.608  -0.608  -0.608  -0.686  -0.686  -0.686
123   S        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
124   S        -0.686  -0.686  -0.686  -0.839  -0.839  -0.839  -0.686  -0.686  -0.686
125   S        -0.686  -0.686  -0.686  -0.839  -0.839  -0.839  -0.686  -0.686  -0.686
126   E        -0.686  -0.686  -0.686   0.065   0.065   0.065  -0.686  -0.686  -0.686
127   A        -0.686  -0.686  -0.686  -0.658  -0.658  -0.658  -0.686  -0.686  -0.686
128   A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
129   S        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
130   S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
131   S        -0.686  -0.686  -0.686  -0.839  -0.839  -0.839  -0.686  -0.686  -0.686
132   K        -0.686  -0.686  -0.686  -0.709  -0.709  -0.709  -0.686  -0.686  -0.686
133   A         1.449   1.449   1.449   0.853   0.853   0.853   1.449   1.449   1.449
134   A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
135   S        -0.686  -0.686  -0.686  -0.839  -0.839  -0.839  -0.686  -0.686  -0.686
136   S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
137   S        -0.686  -0.686  -0.686  -0.839  -0.839  -0.839  -0.686  -0.686  -0.686
138   E        -0.686  -0.686  -0.686  -0.722  -0.722  -0.722  -0.686  -0.686  -0.686
139   A         1.449   1.449   1.449   0.853   0.853   0.853   1.449   1.449   1.449
140   T        -0.686  -0.686  -0.686  -0.117  -0.117  -0.117  -0.686  -0.686  -0.686
141   S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
142   S        -0.686  -0.686  -0.686  -0.948  -0.948  -0.948  -0.686  -0.686  -0.686
143   A         1.449   1.449   1.449   0.853   0.853   0.853   1.449   1.449   1.449
144   A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
145   P        -0.686  -0.686  -0.686  -0.497  -0.497  -0.497  -0.686  -0.686  -0.686
146   S        -0.686  -0.686  -0.686  -0.722  -0.722  -0.722  -0.686  -0.686  -0.686
147   S        -0.686  -0.686  -0.686  -0.709  -0.709  -0.709  -0.686  -0.686  -0.686
148   S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
149   A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
150   A        -0.686  -0.686  -0.686  -0.658  -0.658  -0.658  -0.686  -0.686  -0.686
151   P        -0.686  -0.686  -0.686  -0.670  -0.670  -0.670  -0.686  -0.686  -0.686
152   S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
153   S        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
154   S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
155   A         1.449   1.449   1.449   0.853   0.853   0.853   1.449   1.449   1.449
156   A        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
157   P        -0.686  -0.686  -0.686  -0.670  -0.670  -0.670  -0.686  -0.686  -0.686
158   S        -0.686  -0.686  -0.686  -0.948  -0.948  -0.948  -0.686  -0.686  -0.686
159   S        -0.686  -0.686  -0.686  -1.488  -1.488  -1.488  -0.686  -0.686  -0.686
160   S        -0.686  -0.686  -0.686  -0.839  -0.839  -0.839  -0.686  -0.686  -0.686
161   A        -0.686  -0.686  -0.686  -0.658  -0.658  -0.658  -0.686  -0.686  -0.686
162   E        -0.686  -0.686  -0.686  -0.722  -0.722  -0.722  -0.686  -0.686  -0.686
163   S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
164   S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
165   S        -0.686  -0.686  -0.686  -0.709  -0.709  -0.709  -0.686  -0.686  -0.686
166   K        -0.686  -0.686  -0.686  -0.031  -0.031  -0.031  -0.686  -0.686  -0.686
167   A        -0.686  -0.686  -0.686  -0.658  -0.658  -0.658  -0.686  -0.686  -0.686
168   V         1.449   1.449   1.449   1.503   1.503   1.503   1.449   1.449   1.449
169   S         1.449   1.449   1.449   0.599   0.599   0.599   1.449   1.449   1.449
170   S        -0.686  -0.686  -0.686  -0.722  -0.722  -0.722  -0.686  -0.686  -0.686
171   S        -0.686  -0.686  -0.686  -0.975  -0.975  -0.975  -0.686  -0.686  -0.686
172   V         1.449   1.449   1.449   1.503   1.503   1.503   1.449   1.449   1.449
173   A         1.449   1.449   1.449   0.853   0.853   0.853   1.449   1.449   1.449
174   P         1.449   1.449   1.449   1.780   1.780   1.780   1.449   1.449   1.449
175   T        -0.686  -0.686  -0.686  -0.286  -0.286  -0.286  -0.686  -0.686  -0.686
176   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
177   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
178   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
184   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
185   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
186   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
187   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
188   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
189   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
190   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
195   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
196   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
200   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
201   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
202   G         1.449   1.449   1.449   1.582   1.582   1.582   1.449   1.449   1.449
203   A         1.449   1.449   1.449   0.853   0.853   0.853   1.449   1.449   1.449
204   V         1.449   1.449   1.449   1.503   1.503   1.503   1.449   1.449   1.449
205   V         1.449   1.449   1.449   1.503   1.503   1.503   1.449   1.449   1.449
206   A        -0.686  -0.686  -0.686  -0.658  -0.658  -0.658  -0.686  -0.686  -0.686
207   G        -0.686  -0.686  -0.686  -0.658  -0.658  -0.658  -0.686  -0.686  -0.686
208   A        -0.686  -0.686  -0.686  -0.786  -0.786  -0.786  -0.686  -0.686  -0.686
209   A         1.449   1.449   1.449   0.853   0.853   0.853   1.449   1.449   1.449
210   A        -0.686  -0.686  -0.686  -0.722  -0.722  -0.722  -0.686  -0.686  -0.686
211   L        -0.686  -0.686  -0.686  -0.786  -0.786  -0.786  -0.686  -0.686  -0.686
212   L         1.449   1.449   1.449   1.424   1.424   1.424   1.449   1.449   1.449
213   L        -0.686  -0.686  -0.686  -0.041  -0.041  -0.041  -0.686  -0.686  -0.686
* 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/P27654
Output conservation file - output/P27654
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
