LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss

Vitte, Clémentine; Panaud, Olivier; Quesneville, Hadi

doi:10.1186/1471-2164-8-218

BMC Genomics

Table 2 Global analysis of the Blaster output

From: LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss

		Results from local alignment/reference copy
Family name	Copy nb.	Element size (% of ref. copy size)						Seq. identity/ref. copy
		Min.	1^st Q.	Med.	Mean	3^rd Q.	Max.	Min.	1^st Q.	Med.	Mean	3^rd Q.	Max.
*Osr34*	2107	0.2	1.0	3.8	13.2	12.6	99.3	0.65	0.82	0.87	0.87	0.91	1.00
*Osr30*	1757	0.2	1.1	4.6	15.6	11.4	100.0	0.64	0.83	0.86	0.86	0.88	1.00
*Hopi/Osr27*	1332	0.2	0.5	8.1	29.4	54.2	99.6	0.65	0.85	0.90	0.89	0.95	1.00
*Dagul*	1052	0.2	0.7	4.2	17.1	27.2	100.0	0.66	0.87	0.90	0.90	0.94	1.00
Osr31	986	0.3	1.4	1.9	2.2	2.5	92.4	0.66	0.85	0.87	0.87	0.90	1.00
*Osr14*	934	0.3	2.5	10.3	16.1	27.5	100.0	0.67	0.85	0.89	0.88	0.91	1.00
*Osr40*	855	0.2	1.4	2.9	22.4	28.5	100.0	0.65	0.82	0.86	0.85	0.90	1.00
*Osr8*	831	0.4	3.6	11.0	21.3	19.9	99.9	0.65	0.85	0.89	0.88	0.92	1.00
*Osr37*	565	0.6	3.1	5.0	26.6	49.0	100.0	0.67	0.84	0.86	0.86	0.88	1.00
*Houba/Tos5/Osr13*	563	0.3	4.9	14.9	41.4	96.7	100.0	0.63	0.89	0.94	0.93	0.98	1.00
*Osr29*	446	0.3	3.3	7.1	25.7	37.6	100.0	0.65	0.84	0.87	0.87	0.91	1.00
*Osr1*	269	0.4	1.5	15.1	34.5	69.5	100.0	0.72	0.92	0.94	0.94	0.97	1.00
*RIRE1*	262	0.7	3.1	5.6	14.8	6.7	87.9	0.70	0.84	0.85	0.85	0.86	0.93
*Osr15*	188	0.5	2.0	5.1	19.3	10.8	100.0	0.68	0.87	0.90	0.90	0.94	1.00
*Osr17*	187	0.5	1.1	4.2	31.1	87.2	100.0	0.78	0.87	0.92	0.91	0.95	1.00
Osr23	145	0.5	2.6	4.7	11.8	9.5	100.0	0.71	0.78	0.81	0.81	0.84	1.00
Osr9	119	1.5	7.3	49.1	48.4	87.6	100.0	0.73	0.79	0.84	0.86	0.95	1.00
Osr16	111	0.6	0.7	0.8	2.9	1.5	100.0	0.71	0.89	0.92	0.91	0.94	1.00
*Osr4*	81	0.4	18.2	93.5	64.7	95.2	100.0	0.68	0.94	0.96	0.95	0.98	1.00
Osr10	75	1.4	33.0	98.5	71.8	100.0	100.0	0.70	0.94	0.96	0.93	0.97	1.00
*Osr19*	75	0.4	1.5	2.6	9.8	4.1	100.0	0.75	0.81	0.83	0.84	0.86	1.00
*Osr24*	73	0.6	1.1	2.7	10.1	4.5	100.0	0.73	0.80	0.82	0.83	0.86	1.00
*Osr7*	69	0.4	0.7	1.5	20.4	17.6	100.0	0.70	0.86	0.93	0.91	0.95	1.00
*Osr22*	68	0.5	1.5	2.8	11.3	3.8	87.9	0.73	0.79	0.82	0.82	0.85	1.00
*Osr28*	58	0.2	0.5	1.4	10.1	5.8	100.0	0.63	0.86	0.89	0.88	0.92	1.00
*Osr39*	57	1.0	3.1	4.9	11.9	13.1	100.0	0.69	0.79	0.81	0.81	0.82	1.00
*Osr5*	52	0.9	3.2	11.8	22.2	24.7	100.0	0.73	0.81	0.89	0.88	0.96	1.00
*Osr3*	51	1.3	3.4	19.9	32.9	52.5	100.0	0.65	0.79	0.82	0.82	0.85	1.00
*Osr43*	50	3.0	7.5	8.1	20.6	16.8	100.0	0.72	0.84	0.90	0.89	0.94	1.00
Osr18	34	2.5	5.3	12.6	26.3	37.0	100.0	0.72	0.79	0.82	0.83	0.85	1.00
*Osr36*	34	1.2	2.0	2.9	17.7	14.0	100.0	0.76	0.82	0.85	0.86	0.89	1.00
*Osr6*	27	1.6	4.5	51.5	43.5	77.0	100.0	0.73	0.77	0.82	0.83	0.86	1.00
*Tos17/Osr21*	26	1.7	2.0	5.6	24.0	38.4	100.0	0.64	0.76	0.82	0.83	0.88	1.00
Osr11	25	11.8	70.6	90.1	74.4	93.1	100.0	0.81	0.83	0.85	0.86	0.88	1.00
*Osr42*	21	0.8	1.5	2.4	13.6	3.7	100.0	0.74	0.80	0.82	0.83	0.86	1.00
*Osr35*	18	1.0	2.0	2.6	12.9	7.2	100.0	0.73	0.79	0.82	0.83	0.84	1.00
*Osr44*	18	3.4	8.0	10.6	22.5	21.3	99.9	0.81	0.88	0.92	0.91	0.94	1.00
*Osr12*	16	1.3	2.1	2.4	28.0	57.1	100.0	0.83	0.86	0.88	0.91	1.00	1.00
*Osr2*	13	1.0	1.5	2.8	29.4	70.1	99.3	0.84	0.90	0.92	0.92	0.94	1.00
*Osr38*	13	1.4	2.0	3.2	16.5	10.6	89.3	0.75	0.81	0.81	0.84	0.86	1.00
*Osr20*	11	1.2	2.3	5.5	29.6	52.2	99.9	0.82	0.91	0.94	0.92	0.96	1.00

The elements highlighted in bold correspond to the elements for which the LTR position was validated (see Table 1). ref.: reference; seq.: sequence; nb.:number; ins.: insertion; Min.:minimum; Q.:quartile; Med.:median; Max.:maximum

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ISSN: 1471-2164

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