Table 2.

ATM sequence tracts with lowest mismatch hybridization specificity

Positiona	Sequence	Structureb			Miscalled
		Target	Probe	Repeat type	Probe typec
Sense
883–892	GCCAAAACCC	S	W	Homopolymer	DEL1
2543–2552	AGGTGGAGGA	M	W	(TGGAGG)2	INS
3589–3598d	GTTTCTGAAA	S	S	None	INS
3699–3708d	TTTTCCTTTT	W	W	Homopyrimidine	INS
3919–3928	GGGATGGCAC	M	W	None	INS
4354–4363	GATATAAAAA	W	W	Homopolymer	DEL2
5752–5761	AGACAAAAGA	M	W	Homopolymer	INS
5972–5981	AAAAAAGTAA	W	W	Homopolymer	DEL1
7261–7270	AAAGAGGAAG	M	W	Homopurine	INS
8274–8283	TCCCCTCTCT	W	W	Homopyrimidine	DEL2
8339–8348	TTGTTAACAA	M	W	None	DEL2
8405–8414	AAAAGAAAAT	M	W	Homopurine	DEL1
9122–9131	ACCCCAAAAA	S	W	Homopolymer	DEL1
Antisense
633–642	GGAAAAAAAG	S	W	Homopolymer	INS
822–831	TTCTTTTAAA	S	M	Homopolymer	INS
2403–2412	CAGGAAAAAG	M	W	Homopurine	INS
3589–3598d	TTTCAGAAAC	M	S	None	SUB, DEL1, INS
3699–3708d	AAAAGGAAAA	W	W	Homopurine	INS
8088–8097	TGGTAAATTT	M	W	Homopolymere	DEL1

^aSequence tract where at least eight of 10 bases provided poor hybridization specificity ratios (<1.2-fold) on the indicated strand.

^bStability of potential intramolecular structures that can be formed by the indicated sequence tracts. Mfold (38) was used to predict the intramolecular structures with the lowest Gibbs free energy (ΔG) for either the 25–30 base stretches that encompass each listed sequence tract in the target or for the PM probes complementary to each sequence tract. We use these ΔG values to predict the stability of these structures. ΔG > (−1 kcal/mmol) = weak (W); (−1 kcal/mmol) > ΔG > (−3 kcal/mmol) = medium (M); and ΔG < (−3 kcal/mmol) = strong (S).

^cType of mismatch probe that provided poor hybridization specificity ratios.

^dLow hybridization specificity found on both sense and antisense strands.

^eImmediately following the 3′ end of this segment is a (T)₅ sequence tract.