TABLE 2.

Rearrangement details between O. punctata and O. sativa based on the comparative physical map

		Positions on O. punctata				Positions on O. sativab			e-Value of the alignment of both termini of the rearrangement		Identity of the alignment (%)		Size difference (kb)
Type	Chromosome	Contig	BES (start to end)	CB position	Sizea (kb)	Start (kb)	End (kb)	Size (kb)	Start	End	Start	End
Expansion	2	26	a0052L01f–a0077J24f	200–651	574	15,483	15,545	62	1E-12	1E-1	89	95	512
	3	35, 36	a0057A01r–a0092P04f	364 (ctg35)– 780 (ctg36)	1,139	16,795	17,076	281	1E-63	1E-1	95	93	858
	10	140	a0023E16f–a0078A12f	161–787	796	11,189	11,443	254	1E-117	1E-1	95	94	542
	11	153	a0011F03f–a0042D02r	2088–3218	1,436	11,500	12,132	632	1E-154	1E-4	92	98	804
	11	154	a0067I22r–a0026J19f	1434–2041	772	16,410	16,668	258	1E-111	1E-1	92	97	514
	12	165	a0024O03f–a0079M20f	634–1316	867	10,969	11,196	226	1E-195	1E-1	95	93	641
	12	172	a0089B01f–a0070F24r	968–1541	729	21,182	21,391	209	1E-37	1E-8	91	95	520
Contraction	3	34	a0096I09r–a0079J22r	1210–1260	65	13,378	14,142	764	1E-185	1E-1	95	97	699
	4	44	a0076E21f–a0022J10r	3434–3550	149	7,501	8,342	840	1E-174	1E-1	94	91	692
	4	46	a0016H16r–a0072M08r	3241–3317	98	15,148	15,915	766	1E-162	1E-1	96	92	669
	5	59	a0096F07r–a0080E21r	390–525	173	9,659	10,557	899	1E-91	1E-7	88	90	726
	7	96	a0094P20f–a0091N22f	1178–1300	156	14,383	15,228	845	1E-120	1E-7	90	96	689
	8	106	a0049O07f–a0037I06r	808–1222	527	6,258	7,505	1,247	1E-149	1E-2	94	97	720
	12	172	a0002F15r–a0067E02r	506–666	204	20,247	21,108	861	1E-186	1E-1	96	92	656
Inversion	8	111, 112	a0040E21f–a0073K20r	1820(ctg111)– 784 (ctg111)	1,396	19,648	20,705	1,057	1E-180	1E-1	97	93	—
Transportation	6	75, 76	a0027B15f–a0018I09r	744(ctg75)– 41(ctg76)	544	18,443	18,716	274	1E-126	1E-1	97	95	—

^aBased on 1.27 kb/CB.

^bInternational Rice Genome Sequencing Project (2005).