Schema for RepeatModeler - Transposons Identified by RepeatModeler

Database: DtakGB2 Primary Table: RepeatModeler_DNA Data last updated: 2014-11-20
Big Bed File: /gbdb/DtakGB2/bbi/DtakGB2_DNA.bb
Item Count: 28,096
Format description: RepeatMasker .out record

field	example	description
`chrom`	AFFI02000001	Genomic sequence name
`chromStart`	2079	Start in genomic sequence
`chromEnd`	2115	End in genomic sequence
`name`	rnd-1_family-297	Name of repeat
`score`	0	always 0 place holder
`strand`	+	Relative orientation + or -
`swScore`	234	Smith Waterman alignment score
`milliDiv`	16.7	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`	-17703	-#bases after match in genomic sequence
`repClass`	DNA	Class of repeat
`repFamily`	MITE	Family of repeat
`repStart`	1	Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence
`repEnd`	36	End in repeat sequence
`repLeft`	-548	-#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
AFFI02000001	2079	2115	rnd-1_family-297	+	234	16.7	0.0	0.0	-17703	DNA	MITE	1	36	-548
AFFI02000001	3644	4137	rnd-1_family-165	-	4093	3.7	0.2	0.4	-15681	DNA	MITE	0	492	1
AFFI02000001	4286	4349	rnd-1_family-94	-	369	6.5	1.6	1.6	-15469	DNA	DNA	-242	630	568
AFFI02000001	4817	5096	rnd-1_family-94	-	2473	2.1	0.7	0.0	-14722	DNA	DNA	-295	577	297
AFFI02000001	5096	5158	rnd-1_family-185	-	472	6.5	9.7	0.0	-14660	DNA	MITE	-1	187	120
AFFI02000001	7741	7852	rnd-1_family-185	-	854	3.6	9.0	0.0	-11966	DNA	MITE	-67	121	1
AFFI02000001	7852	7907	rnd-1_family-94	-	471	1.6	0.0	0.0	-11911	DNA	DNA	-581	291	237
AFFI02000001	8614	8852	rnd-1_family-94	-	1817	5.1	0.4	0.8	-10966	DNA	DNA	-634	238	2
AFFI02000001	9289	9587	rnd-5_family-2565	-	484	28.5	3.0	4.8	-10231	DNA	CMC-EnSpm	-401	2183	1891
AFFI02000001	10481	11351	rnd-5_family-2565	-	2210	27.1	7.5	3.9	-8467	DNA	CMC-EnSpm	-870	1714	815

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