Table 1.

mtDNA deletion sizes in COX-deficient fibre regions as determined by PCR/gel electrophoresis and mtDNA breakpoint sequencing

COX- deficient fibre	Estimated mtDNA deletion length (kb)	Verified mtDNA deletion length (bp)	Size difference (bp)	5′ Deletion breakpoint	5′ Breakpoint sequence	3′ Deletion breakpoint	3′ Breakpoint sequence	Breakpoint repeat type
1	3.5	3715	215	9576	atcaccccgc	13 291	acaatcggca	No repeat
2	3.5	3904	404	10 265	tctagaaatt	14 269	atcctcccga	No repeat
3	5	4977	23	8482	tccctcacca	13 459	tccctcacca	Direct repeat
4	6.5	6994	444	9075	aatatcaacc	16 069	aagtattgac	No repeat
5	7	7479	479	7939	actaatcttc	15 436	agacgccctc	Imperfect repeat (4/10)
6	7.5	7648	148	6341	agacctaacc	13 989	gcccctactc	Imperfect repeat (5/10)
7	8.5	8493	7	5438	aaaacccacc	13 931	accctagcat	No repeat
8	9	9033	33	6558	aacaccacct	15 591	caattctccg	Imperfect repeat (4/10)
9	9	9026	26	6634	ctgaagttta	15 660	caataatccc	No repeat
10	9	9120	120	6468	tgatccgtcc	15 588	acacaattct	No repeat
11	2.5	2880	120	7236	gactaccccg	9516	ttttaccact	Imperfect repeat (5/10)
12	5	4977	23	8482	tccctcacca	13 459	tccctcacca	Direct repeat
13	6	5647	353	7406	ccccccaccc	13 053	catagaaggc	No repeat
14	6.5	6175	325	7947	tcaactccta	14 122	ttcccactca	Imperfect repeat (4/10)
15	7.5	7046	464	5787	aagctgcttc	12 833	atgccaacac	Imperfect repeat (4/10)
16	9.5	9044	456	6105	ataatcttct	15 149	gtcctcccgt	Imperfect repeat (4/10)
17	10	9846	154	5341	ttaacctcta	15 187	agtaattaca	No repeat
18	6.5	6927	427	8734	acctgatctc	15 661	aataatcccc	No repeat
19	8	8026	26	7634	tcccctatca	15 660	caataatccc	No repeat
20	3	3250	250	12 140	tcctcttgta	15 390	cctcccattc	No repeat

COX-deficient fibres 1–10 were small COX-deficient fibres, while 11–20 were large COX-deficient fibres. Estimated mtDNA deletion length refers to mtDNA deletion size as measured to the nearest 0.5 kb by long-range PCR and gel electrophoresis, while verified mtDNA deletion size refers to the deletion size ascertained by breakpoint sequencing; size difference refers to any discrepancy between the estimated and verified mtDNA deletion sizes in base-pairs. mtDNA sequences of 10 bp are supplied 5′ and 3′ of the mtDNA deletion, with repeated bases in bold and italicized. Two direct repeats (identical flanking sequences) and seven imperfect repeats (4–9 bp repeated between flanking sequences) were identified.