Transposable Elements

Transposons where detected and classified by an homology search against the REdat_9.7_Poaceae section of the PGSB transposon library [pmid 26527721].
The program vmatch (http://www.vmatch.de) was used for that purpose as a fast and efficient matching tool suited for large and highly repetitive genomes with
the following parameters: identity>=70%, minimal hit length 75 bp, seedlength 12 bp (exact commandline: -d -p -l 75 -identity 70 -seedlength 12 -exdrop 5).To
obtain an overlap free annotation the vmatch output was filtered for redundant hits via a priority based approach. Higher scoring matches where assigned first
and lower scoring hits at overlapping positions where either shortened (<90% coverage and >=50bp rest length) or removed.

Hover over the different structures in the image below to see more information in the tooltip.

TE 3-Letter Code	TE Class	REdat Name	REcat Key	TE Name	AGP Chromosome	AGP Start	AGP End	Strand	TE ID	Identity Percent	Coverage Percent
RLG	Gypsy	LTR_HVVMRXALLeA0222A01_ipk17_c1_1662	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26605	chr4H	196,531,252	196,541,531	Reverse	3848135	93.23	100.0
RLC	Copia	LTR_HVVMRXALLhC0040A01_v49_c1_3273	02.01.01.05.01	RLC_Bare_HvMo_chr_4H-1890	chr4H	196,332,312	196,341,241	Reverse	3848136	98.07	100.0
RLC	Copia	LTR_HVVMRXALLmA0188O01_v59_c1_3490	02.01.01.05.01	RLC_Bare_HvMo_chr_4H-1891	chr4H	196,411,175	196,420,096	Forward	3848137	97.16	100.0
RLC	Copia	LTR_HVVMRXALLeA0273I21_ipk18_c3_1747	02.01.01.05.99	RLC_unknown_HvMo_chr_4H-14564	chr4H	196,203,302	196,212,155	Reverse	3848138	96.3	61.51
RLG	Gypsy	LTR_HVVMRXALLeA0064K01_v50_c2_1288	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26352	chr4H	196,027,413	196,036,480	Reverse	3848139	91.4	64.39
RLX	LTR	LTR_HVVMRXALLeA0168D20_ipk8_c1_1541	02.01.01.99	RLX_unknown_HvMo_chr_4H-51914	chr4H	196,024,672	196,027,412	Reverse	3848140	88.45	64.64
RLX	LTR	LTR_HVVMRXALLmA0120E01_v59_c1_3455	02.01.01.99	RLX_unknown_HvMo_chr_4H-51902	chr4H	195,980,259	195,988,533	Reverse	3848141	92.09	81.67
RLC	Copia	LTR_HVVMRXALLeA0333N24_ipk10_c2_1813	02.01.01.05.01	RLC_Bare_HvMo_chr_4H-1892	chr4H	196,459,125	196,466,800	Reverse	3848142	96.32	86.15
RLX	LTR	LTR_HVVMRX83KhA0059D03_ipk5_c2_182	02.01.01.99	RLX_unknown_HvMo_chr_4H-51947	chr4H	196,095,944	196,104,398	Reverse	3848143	89.91	89.5
RLX	LTR	LTR_HVVMRXALLhA0620I09_v39_c2_2852	02.01.01.99	RLX_unknown_HvMo_chr_4H-51870	chr4H	195,889,807	195,897,290	Forward	3848144	94.93	87.44
RLC	Copia	LTR_HVVMRXALLeA0333N24_ipk10_c2_1813	02.01.01.05.01	RLC_Bare_HvMo_chr_4H-1893	chr4H	196,466,950	196,473,831	Reverse	3848145	96.64	78.98
RLC	Copia	LTR_HVVMRXALLhA0754K24_v2_c2_3063	02.01.01.05.99	RLC_unknown_HvMo_chr_4H-14548	chr4H	196,068,896	196,076,716	Reverse	3848147	88.66	88.11
RLG	Gypsy	LTR_HVVMRXALLeA0216O01_v58_c1_1650	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26348	chr4H	196,009,328	196,017,443	Reverse	3848148	83.71	38.41
RLX	LTR	LTR_HVVMRXALLhA0418F22_v5_c1_2569	02.01.01.99	RLX_unknown_HvMo_chr_4H-52049	chr4H	196,324,769	196,332,144	Reverse	3848149	87.99	53.66
RLX	LTR	LTR_HVVMRXALLhA0335G24_v7_c2_2395	02.01.01.99	RLX_unknown_HvMo_chr_4H-52006	chr4H	196,201,134	196,203,109	Reverse	3848150	90.36	48.78
RLG	Gypsy	LTR_HVVMRXALLeA0216O01_v58_c1_1650	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26420	chr4H	196,298,876	196,306,025	Reverse	3848151	88.2	33.83
RLG	Gypsy	LTR_HVVMRXALLmA0120E01_v59_c2_3456	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26421	chr4H	196,306,026	196,312,634	Reverse	3848152	90.88	46.05
RLX	LTR	LTR_HVVMRX83KhA0172K23_ipk4_c3_570	02.01.01.99	RLX_unknown_HvMo_chr_4H-51960	chr4H	196,119,913	196,126,590	Forward	3848154	87.41	76.75
RLX	LTR	LTR_HVVMRXALLhA0623B12_v39_c4_2857	02.01.01.99	RLX_unknown_HvMo_chr_4H-51915	chr4H	196,038,431	196,044,373	Forward	3848156	92.85	31.25
RLC	Copia	LTR_HVVMRXALLhA0727F08_v26_c1_3019	02.01.01.05.99	RLC_unknown_HvMo_chr_4H-14563	chr4H	196,197,815	196,201,074	Reverse	3848157	91.77	41.84
RLC	Copia	LTR_HVVMRXALLeA0067O06_ipk2_c2_1301	02.01.01.05.99	RLC_unknown_HvMo_chr_4H-14536	chr4H	195,905,405	195,910,888	Forward	3848158	95.68	85.26
RLX	LTR	LTR_HVVMRXALLhA0545O15_v1_c1_2750	02.01.01.99	RLX_unknown_HvMo_chr_4H-52028	chr4H	196,269,372	196,276,106	Reverse	3848159	81.1	47.92
RLX	LTR	LTR_HVVMRX83KhA0012D03_v72_c1_51	02.01.01.99	RLX_unknown_HvMo_chr_4H-52118	chr4H	196,551,885	196,557,070	Forward	3848160	92.92	23.86
RLC	Copia	LTR_HVVMRXALLeA0012N09_ipk2_c1_1206	02.01.01.05.99	RLC_unknown_HvMo_chr_4H-14558	chr4H	196,172,741	196,178,335	Reverse	3848163	86.65	63.33
RLC	Copia	LTR_HVVMRX83KhA0162E17_v54_c2_505	02.01.01.05.99	RLC_unknown_HvMo_chr_4H-14541	chr4H	195,956,955	195,962,059	Reverse	3848165	90.11	57.19
RLX	LTR	LTR_HVVMRXALLmA0252O01_v61_c1_3538	02.01.01.99	RLX_unknown_HvMo_chr_4H-52074	chr4H	196,389,489	196,394,928	Reverse	3848166	86.07	41.55
RLG	Gypsy	LTR_HVVMRXALLrA0093C09_ipk21_c4_3830_2frag	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26563	chr4H	196,482,893	196,487,695	Reverse	3848167	92.28	34.16
RLX	LTR	LTR_HVVMRXALLeA0178E11_ipk8_c1_1568	02.01.01.99	RLX_unknown_HvMo_chr_4H-51987	chr4H	196,163,215	196,168,925	Reverse	3848168	82.93	27.93
RLG	Gypsy	LTR_HVVMRXALLrA0093C09_ipk21_c4_3830_2frag	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26601	chr4H	196,521,277	196,527,176	Reverse	3848169	80.73	41.78
RLX	LTR	LTR_HVVMRXALLeA0109E18_ipk7_c2_1379	02.01.01.99	RLX_unknown_HvMo_chr_4H-51864	chr4H	195,867,874	195,872,502	Reverse	3848170	93.04	67.56
RLG	Gypsy	LTR_HVVMRX83KhA0051L21_v72_c1_140	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26347	chr4H	195,997,126	196,001,624	Reverse	3848171	94.93	21.67
RLX	LTR	LTR_HVVMRXALLeA0066N18_ipk6_c1_1293	02.01.01.99	RLX_unknown_HvMo_chr_4H-51948	chr4H	196,104,483	196,105,384	Reverse	3848175	90.07	57.59
RLG	Gypsy	LTR_HVVMRX83KhA0071K21_v55_c2_243	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26398	chr4H	196,276,107	196,277,639	Reverse	3848176	85.55	42.93
RLX	LTR	LTR_HVVMRX83khA0082H11_v68_c1_873	02.01.01.99	RLX_unknown_HvMo_chr_4H-52060	chr4H	196,367,346	196,372,313	Forward	3848177	85.02	100.0
RLX	LTR	LTR_HVVMRX83KhA0092C20_ipk10_c3_292	02.01.01.99	RLX_unknown_HvMo_chr_4H-52083	chr4H	196,439,179	196,444,007	Reverse	3848178	85.28	36.89
RLX	LTR	LTR_HVVMRX83KhA0094K20_v62_c1_299	02.01.01.99	RLX_unknown_HvMo_chr_4H-51943	chr4H	196,084,213	196,088,221	Reverse	3848180	92.32	47.95
RLG	Gypsy	LTR_HVVMRXALLeA0132N09_ipk2_c3_1440_2frag	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26564	chr4H	196,487,696	196,491,649	Reverse	3848181	91.69	28.32
RLG	Gypsy	LTR_HVVMRXALLmA0018O09_ipk24_c1_3351	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26373	chr4H	196,168,926	196,169,913	Reverse	3848182	72.38	50.14
RLX	LTR	LTR_HVVMRX83khA0057C14_v64_c1_782	02.01.01.99	RLX_unknown_HvMo_chr_4H-52055	chr4H	196,353,152	196,358,147	Forward	3848183	79.62	22.94
RLG	Gypsy	trep3259	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26500	chr4H	196,444,008	196,444,787	Reverse	3848184	83.74	34.66
RLC	Copia	trep3134	02.01.01.05.99	RLC_unknown_HvMo_chr_4H-14542	chr4H	195,962,697	195,965,794	Reverse	3848185	92.16	43.92
RLC	Copia	LTR_HVVMRXALLhA0340A23_v5_c1_2413	02.01.01.05.99	RLC_unknown_HvMo_chr_4H-14559	chr4H	196,178,961	196,179,711	Reverse	3848187	80.29	53.02
RLX	LTR	LTR_HVVMRX83KhA0010A07_v72_c1_38	02.01.01.99	RLX_unknown_HvMo_chr_4H-52016	chr4H	196,231,063	196,234,890	Forward	3848189	89.0	29.33
RLG	Gypsy	trep2346	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26386	chr4H	196,234,891	196,236,605	Forward	3848190	87.04	51.41
RLX	LTR	LTR_HVVMRX83KhA0012D03_v72_c1_51	02.01.01.99	RLX_unknown_HvMo_chr_4H-52140	chr4H	196,610,695	196,614,248	Reverse	3848191	90.2	16.39
RLX	LTR	LTR_HVVMRXALLhA0426C16_v7_c1_2582	02.01.01.99	RLX_unknown_HvMo_chr_4H-51933	chr4H	196,060,742	196,064,218	Reverse	3848192	91.14	38.99
RLX	LTR	LTR_HVVMRXALLrA0090C01_v49_c1_3825	02.01.01.99	RLX_unknown_HvMo_chr_4H-52027	chr4H	196,264,205	196,267,666	Reverse	3848193	90.91	42.25
RLG	Gypsy	LTR_HVVMRXALLeA0064K01_v50_c2_1288	02.01.01.10.99	RLG_unknown_HvMo_chr_4H-26399	chr4H	196,277,640	196,280,005	Reverse	3848194	80.45	29.57
RLX	LTR	LTR_HVVMRXALLhA0545O15_v1_c1_2750	02.01.01.99	RLX_unknown_HvMo_chr_4H-52094	chr4H	196,479,735	196,482,892	Reverse	3848195	91.68	22.74
RLX	LTR	LTR_HVVMRXALLhA0406K20_v15_c1_2554	02.01.01.99	RLX_unknown_HvMo_chr_4H-51869	chr4H	195,888,736	195,889,806	Forward	3848196	92.14	36.9

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TE Positions

Transposable elements