Identification and utilization of arbitrary correlations in models of recombination signal sequences

Table 1 Strongest nucleotide associations in 12-RSS

Correlated positions	Associated nucleotides	Count	Frequency
7:8:19	G:A:A	73	0.365
	G:C:T	23	0.115
	G:C:A	17	0.085
	G:A:G	11	0.055
	A:G:G	10	0.05
	G:A:T	9	0.045
	A:G:C	6	0.03
	A:T:T	6	0.03
	G:T:T	6	0.03
	G:G:A	5	0.025
	A:A:T	4	0.02
	A:C:T	4	0.02
	A:G:T	3	0.015
	G:A:C	2	0.01
	G:C:G	2	0.01
	G:T:G	2	0.01
	C:A:T	2	0.01
	C:T:G	2	0.01
	C:T:C	2	0.01
	T:A:T	2	0.01
	A:A:A	1	0.005
	G:G:C	1	0.005
	G:G:T	1	0.005
	G:C:C	1	0.005
	C:A:A	1	0.005
	C:G:G	1	0.005
	C:C:C	1	0.005
	C:C:T	1	0.005
	C:T:T	1	0.005
16:17:18	C:T:T	34	0.169
	C:A:T	32	0.159
	T:G:G	20	0.1
	T:C:C	15	0.075
	C:T:G	14	0.07
	C:C:T	11	0.055
	A:G:C	9	0.045
	T:T:C	8	0.04
	C:T:C	7	0.035
	T:A:G	7	0.035
	C:C:A	5	0.025
	C:A:G	4	0.02
	T:C:T	4	0.02
	T:G:A	3	0.015
	A:T:C	2	0.01
	G:G:G	2	0.01
	C:A:C	2	0.01
	C:C:G	2	0.01
	C:C:C	2	0.01
	T:A:C	2	0.01
	T:A:T	2	0.01
	T:G:T	2	0.01
	T:C:A	2	0.01
	A:A:C	1	0.005
	A:C:T	1	0.005
	A:T:A	1	0.005
	G:C:T	1	0.005
	G:T:C	1	0.005
	C:A:A	1	0.005
	C:T:A	1	0.005
	T:A:A	1	0.005
	T:T:A	1	0.005
	T:T:G	1	0.005
20:21:22	A:C:A	157	0.785
	G:C:A	18	0.09
	T:C:A	6	0.03
	C:C:C	3	0.015
	A:A:A	2	0.01
	G:A:C	2	0.01
	G:G:T	2	0.01
	G:T:C	2	0.01
	A:C:T	1	0.005
	G:A:G	1	0.005
	G:A:T	1	0.005
	C:A:A	1	0.005
	C:A:G	1	0.005
	C:C:A	1	0.005
	T:C:G	1	0.005
	T:T:C	1	0.005

For the three groups of positions in the 12-RSS model exhibiting the strongest correlations, the nucleotide motifs present in our dataset at those positions, the number of RSS containing that motif, and the frequency in the dataset are shown. Nucleotide motifs not shown do not occur in our dataset. For example, three positions making up one group (for example, 7, 8 and 19) would be occupied in each RSS by one of the 64 triplets, but not every one of the 64 triplets will be present.

ISSN: 1474-760X