Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DsuzGB1 Primary Table: RepeatModeler_LTR Data last updated: 2014-11-20
Big Bed File: /gbdb/DsuzGB1/bbi/DsuzGB1_LTR.bb
Item Count: 46,607
Format description: RepeatMasker .out record

field	example	description
`chrom`	AWUT01012676	Genomic sequence name
`chromStart`	63043	Start in genomic sequence
`chromEnd`	63416	End in genomic sequence
`name`	rnd-6_family-2699	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	2390	Smith Waterman alignment score
`milliDiv`	9.9	Base mismatches in parts per thousand
`milliDel`	4.6	Bases deleted in parts per thousand
`milliIns`	0.0	Bases inserted in parts per thousand
`genoLeft`	-31179	-#bases after match in genomic sequence
`repClass`	LTR	Class of repeat
`repFamily`	Gypsy	Family of repeat
`repStart`	-524	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	543	End in repeat sequence
`repLeft`	154	-#bases after match (if strand is +) or start (if strand is -) in repeat sequence

Sample Rows

chrom	chromStart	chromEnd	name	strand	swScore	milliDiv	milliDel	milliIns	genoLeft	repClass	repFamily	repStart	repEnd	repLeft
AWUT01012676	63043	63416	rnd-6_family-2699	-	2390	9.9	4.6	0.0	-31179	LTR	Gypsy	-524	543	154
AWUT01012676	64496	64874	rnd-1_family-814	+	3270	0.5	0.0	0.0	-29721	LTR	Gypsy	1	378	0
AWUT01012676	64877	64939	rnd-1_family-700	+	280	19.4	3.2	0.0	-29656	LTR	Pao	635	698	-223
AWUT01012676	64914	64982	rnd-1_family-907	+	399	11.8	1.5	0.0	-29613	LTR	Pao	187	255	-27
AWUT01012676	65407	65695	rnd-1_family-293	+	2158	2.8	0.3	1.1	-28900	LTR	Pao	295	580	0
AWUT01012676	66500	66996	rnd-1_family-130	+	3925	4.6	0.0	0.0	-27599	LTR	Pao	1	496	-501
AWUT01012676	67002	67074	rnd-1_family-227	+	599	2.8	0.0	0.0	-27521	LTR	Pao	38	109	-545
AWUT01012676	67079	67142	rnd-1_family-227	+	461	6.3	0.0	0.0	-27453	LTR	Pao	266	328	-326
AWUT01012676	67142	68430	rnd-1_family-138	+	7425	4.7	1.4	0.0	-26165	LTR	Pao	1	1190	0
AWUT01012676	68255	68650	rnd-1_family-142	-	3119	5.3	0.0	0.0	-25945	LTR	Pao	-2	1065	671

RepeatModeler (RepeatModeler) Track Description


	Description This track shows the transposon fragments identified by RepeatMasker using the species-specific RepeatModeler library constructed by the GEP. The consensus sequences produced by RepeatModeler were reclassified using the protocol described in the supplemental methods section. References Smit, AFA, Hubley, R. RepeatModeler Open-1.0. http://www.repeatmasker.org. 2008-2010. Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010.

Description

References