Table 3.

Overall frequency of hexanucleotides around primary nicking sites associated with 400 Alu and ID sequences

Frequency	Hexamer(s)
53	TTAAAA
38	TTAAGA
32	TTAGAA
17	TTGAAA
11	TTAAAG
10	CTAAAA
9	TCAAGA
8	AAAAAA
7	TTTAAA
6	TAAAAA, GTAAGA
5	TTAAAT, TCAGAA, TCAAAA, GTAAAG
4	TTAAGT, TCTAAA, GTAGAA, GTAAAA, ATAGAA, AAAAAT
3	TTAACA, TGAAAA, TAAAAG, GTGAAA, CTAAAG, CCAAAA
2	TTTAAT, TTATAA, TTAGAT, TTAGAG, TGAGAA, TGAAAT, TGAAAG, TCAAAT, TAAGAA, GGAAAA, GAAAAT, GAAAAG, GAAAAA, CTAAGA, CAAAAA, ATAAGA, ATAAAA, AGAAGT, AGAAAG, ACAAAA, AAAGTT, AAAATC, AAAATA, AAAAAG
1	TTTTTT, TTTTTC, TTTTAA, TTTGAT, TTTAGA, TTGGAA, TTGAGG, TTATGT, TTAGGA, TTAATT, TTAATC, TTAAAC, TGTTCA, TGTATA, TGGTGA, TGAAGA, TCAGAG, TCAACA, TCAAAG, TCAAAC, TATTAA, TATAAA, TAGAAG, TAAGTG, TAAGGA, TAAGAG, TAAAAC, GTTAAA, GTGAGA, GTAGAC, GTAATG, GGGGGT, GGAGGA, GGAGAA, GGACTG, GGAAAG, GGAAAC, GCAGTT, GCAGAA, GCAAGA, GCAAAG, GCAAAA, GATGCT, GAATGC, GAAGAG, GAAAGT, GAAAAC, CTCAAG, CTATAA, CTAGAA, CTAAGC, CCTGTG, CCATTA, CCATAA, CCAATG, CCAATA, CCAAGA, CATAAA, CAGAAG, CACAGA, CAATTA, CAAGAG, CAAACT, ATTTCA, ATGAGC, ATGAGA, ATGAAA, AGTTTT, AGTAAA, AGCATA, AGAAGA, AGAAAA, ACTAAA, ACAGAA, AATTTT, AATTAC, AAGGGG, AAGCTT, AAGATG, AAGAGT, AAGAAA, AAATGT, AAATCT, AAATAA, AAAGTA, AAAGCT, AAAGAG, AAAGAA, AAACAT, AAACAC, AAAATG, AAAAGT, AAAAGG

All hexamers include two bases preceding and four bases following the 5′ ends of the flanking repeats.