Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DsuzGB1 Primary Table: RepeatModeler_LINE Data last updated: 2014-11-20
Big Bed File: /gbdb/DsuzGB1/bbi/DsuzGB1_LINE.bb
Item Count: 36,825
Format description: RepeatMasker .out record

field	example	description
`chrom`	AWUT01012676	Genomic sequence name
`chromStart`	16851	Start in genomic sequence
`chromEnd`	17316	End in genomic sequence
`name`	rnd-1_family-89	Name of repeat
`score`	0	always 0 place holder
`strand`	-	Relative orientation + or -
`swScore`	3463	Smith Waterman alignment score
`milliDiv`	3.7	Base mismatches in parts per thousand
`milliDel`	8.8	Bases deleted in parts per thousand
`milliIns`	0.2	Bases inserted in parts per thousand
`genoLeft`	-77279	-#bases after match in genomic sequence
`repClass`	LINE	Class of repeat
`repFamily`	LINE	Family of repeat
`repStart`	0	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	882	End in repeat sequence
`repLeft`	378	-#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	16851	17316	rnd-1_family-89	-	3463	3.7	8.8	0.2	-77279	LINE	LINE	0	882	378
AWUT01012676	17339	18678	rnd-1_family-56	+	6150	7.7	4.2	0.1	-75917	LINE	LINE	1	1669	0
AWUT01012676	18678	19142	rnd-1_family-56	+	3464	4.7	6.0	0.0	-75453	LINE	LINE	597	1088	-336
AWUT01012676	19155	20307	rnd-1_family-76	-	8326	7.2	2.4	0.2	-74288	LINE	LINE	-128	1177	1
AWUT01012676	19690	20980	rnd-1_family-68	+	8977	7.4	1.6	0.2	-73615	LINE	LINE	1	1254	0
AWUT01012676	20982	21378	rnd-1_family-88	+	2903	5.3	3.5	0.2	-73217	LINE	LINE	223	631	-163
AWUT01012676	27183	27338	rnd-1_family-335	+	243	34.8	6.5	0.0	-67257	LINE	LINE	290	454	-294
AWUT01012676	27884	27945	rnd-1_family-351	+	272	26.2	0.0	0.0	-66650	LINE	LINE	280	340	-241
AWUT01012676	28052	28229	rnd-1_family-396	+	274	31.4	5.1	0.0	-66366	LINE	LINE	251	562	0
AWUT01012676	28995	29187	rnd-1_family-335	+	463	33.3	2.1	0.0	-65408	LINE	LINE	235	430	-318

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