Schema for RepBase Repeats - RepeatMasker using RepBase Drosophila Repeat Library

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Schema for RepBase Repeats - RepeatMasker using RepBase Drosophila Repeat Library

Database: DmojImproved Primary Table: RepBase Row Count: 69,464

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	10	`int(10) unsigned`	range
`chromEnd`	523	`int(10) unsigned`	range
`name`	Homo6	`varchar(255)`	values
`score`	3365	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	10	`int(10) unsigned`	range
`thickEnd`	523	`int(10) unsigned`	range
`itemRgb`	8388608	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	513	`longblob`
`chromStarts`	0	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	itemRgb	blockCount	blockSizes	chromStarts
585	improved_6498	10	523	Homo6	3365	-	10	523	128,0,0	1	513	0
585	improved_6498	516	10077	Homo6	1644	-	516	10077	128,0,0	3	59,193,512	0,59,9049
585	improved_6498	1277	4455	DMRT1C	1051	+	1277	4455	0,0,128	2	265,2699	0,479
585	improved_6498	6026	9246	DMRT1C	634	+	6026	9246	0,0,128	3	319,1788,890	0,510,2330
585	improved_6498	9290	9370	Homo6	419	-	9290	9370	128,0,0	1	80	0
585	improved_6498	10077	10131	Helitron-1_DVir	352	-	10077	10131	230,85,13	1	54	0
585	improved_6498	10129	14839	Homo6	2421	-	10129	14839	128,0,0	2	193,593	0,4117
585	improved_6498	11031	14094	DMRT1C	533	+	11031	14094	0,0,128	3	350,1669,783	0,494,2280
585	improved_6498	14138	14218	Homo6	419	-	14138	14218	128,0,0	1	80	0
585	improved_6498	14880	15073	Homo6	1359	-	14880	15073	128,0,0	1	193	0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RepBase Repeats (RepBase) Track Description


	Description This track was created by using Arian Smit's RepeatMasker program, which screens DNA sequences for interspersed repeats and low complexity DNA sequences. The program outputs a detailed annotation of the repeats that are present in the query sequence (represented by this track), as well as a modified version of the query sequence in which all the annotated repeats have been masked. RepeatMasker uses the Repbase Update library of repeats from the Genetic Information Research Institute (GIRI). Repbase Update is described in Jurka (2000) in the References section below. Credits Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and repeat libraries used to generate this track. References Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. http://www.repeatmasker.org. 1996-2010. Jurka J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 2000 Sep;16(9):418-420.