Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DbipGB2 Primary Table: RepeatModeler_SINE Data last updated: 2014-11-20
Big Bed File: /gbdb/DbipGB2/bbi/DbipGB2_SINE.bb
Item Count: 24
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFE02003129	Genomic sequence name
`chromStart`	18585	Start in genomic sequence
`chromEnd`	18624	End in genomic sequence
`name`	rnd-5_family-6343	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	264	Smith Waterman alignment score
`milliDiv`	2.6	Base mismatches in parts per thousand
`milliDel`	0.0	Bases deleted in parts per thousand
`milliIns`	0.0	Bases inserted in parts per thousand
`genoLeft`	-6222	-#bases after match in genomic sequence
`repClass`	SINE	Class of repeat
`repFamily`	SINE	Family of repeat
`repStart`	113	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	151	End in repeat sequence
`repLeft`	0	-#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
AFFE02003129	18585	18624	rnd-5_family-6343	0	+	264	2.6	0.0	0.0	-6222	SINE	SINE	113	151	0

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