Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DkikGB2 Primary Table: RepeatModeler_LTR Data last updated: 2014-11-20
Big Bed File: /gbdb/DkikGB2/bbi/DkikGB2_LTR.bb
Item Count: 13,752
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFH02000009	Genomic sequence name
`chromStart`	9	Start in genomic sequence
`chromEnd`	294	End in genomic sequence
`name`	rnd-1_family-54	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	947	Smith Waterman alignment score
`milliDiv`	22.9	Base mismatches in parts per thousand
`milliDel`	0.8	Bases deleted in parts per thousand
`milliIns`	2.3	Bases inserted in parts per thousand
`genoLeft`	-789	-#bases after match in genomic sequence
`repClass`	LTR	Class of repeat
`repFamily`	Pao	Family of repeat
`repStart`	230	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	507	End in repeat sequence
`repLeft`	-221	-#bases after match (if strand is +) or start (if strand is -) in repeat sequence

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	swScore	milliDiv	milliDel	milliIns	genoLeft	repClass	repFamily	repStart	repEnd	repLeft
AFFH02000009	9	294	rnd-1_family-54	0	+	947	22.9	0.8	2.3	-789	LTR	Pao	230	507	-221
AFFH02000009	527	1025	rnd-1_family-112	0	+	1138	23.9	5.7	3.4	-58	LTR	Pao	41	516	-150

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