Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton Gossypium raimondii by Comparative Genomics Approaches

Table 7

Distribution of repeats (>100 bp) in G. raimondii mt genome.

Number	Size (bp)	Identity (%)	Copy-1		Copy-2		Copy-3		Type
			Start	End	Start	End	Start	End
R1	63905	99.93	50881	114784	502128	565987			DR
R2	10624	99.94	248091	258714	405137	415754			DR
R3	9130	99.97	22950	32078	183392	174264			IR
R4	2532	99.64	499598	502127	673553	676077			DR
R5	767	98.57	141082	141848	440545	441311			DR
R6	596	90.44	257539	258122	414581	415163	646113	646685	DR
R7	504	98.21	33537	34040	142948	143451			DR
R8	380	82.11	52465	52834	389903	389536	503712	504081	IR/DR
R9	349	99.71	167653	168001	257539	257191	414581	414233	IR
R10	314	96.18	52965	53273	338227	338539	504212	504520	DR
R11	260	86.54	281040	281285	402396	402148			IR
R12	257	100	47863	48119	256882	257138	413924	414180	DR
R13	229	100	125112	125340	224959	225187			DR
R14	211	98.58	34589	34797	656235	656025			IR
R15	209	92.34	329404	329606	670726	670933			DR
R16	208	83.17	100270	100476	434363	434173	551480	551686	IR/DR
R17	194	100	28320	28513	177828	178021	652575	652768	DR
R18	194	92.78	378565	378750	656201	656010			IR
R19	175	100	378665	378839	493129	492955			IR
R20	174	99.43	276747	276920	338558	338731			DR
R21	172	90.7	261988	262155	604442	604271			IR
R22	165	98.18	369418	369582	652955	652791			IR
R23	165	93.94	84343	84505	478354	478516	535576	535738	DR
R24	162	97.53	258147	258306	322746	322905	415187	415346	DR
R25	156	97.44	34621	34774	378565	378719			DR
R26	148	89.86	604752	604898	673561	673425			IR
R27	145	87.59	236506	236650	634479	634615			DR
R28	142	99.3	32393	32534	142478	142619			DR
R29	137	95.62	59169	59304	260007	259872	510413	510548	IR/DR
R30	133	95.49	478656	478788	576482	576614			DR
R31	126	89.68	303621	303744	378711	378588			IR
R32	120	82.5	402261	402378	650464	650573			DR
R33	118	99.15	83712	83829	455331	455448	534945	535062	DR
R34	118	84.75	259617	259733	338550	338658			DR
R35	117	94.02	281058	281174	650573	650460			IR
R36	117	87.18	354	470	277212	277321			DR
R37	115	87.83	337542	337645	604839	604725			IR
R38	113	100	167103	167215	321673	321785			DR
R39	112	97.32	81756	81866	162601	162711			DR
R40	112	85.71	84872	84974	279997	280107	536105	536207	DR
R41	111	98.2	162601	162711	532995	533104			DR
R42	110	86.36	259625	259733	276747	276847			DR
R43	107	100	28258	28364	177977	178083	385823	385717	DR/IR
R44	106	94.34	4873	4976	351331	351226			IR
R45	104	99.04	115134	115237	646183	646080			IR
R46	102	94.12	404656	404756	587091	586991			IR
R47	100	84	416288	416387	493179	493089			DR/IR
R48	100	85	76812	76904	396912	397011	528052	528144	DR
R	85	97.65	384090	384173	454437	454353			IR

Boldface indicates IR copy, compared with copy-1 as control.
DR and IR: direct and inverted repeats, respectively.
IR/DR or DR/IR: both direct repeat and inverted repeat among multiple copies.