Schema for Inverted Repeats - Inverted Repeats Identified by Inverted Repeats Finder

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Schema for Inverted Repeats - Inverted Repeats Identified by Inverted Repeats Finder

Database: DmojImproved Primary Table: irf Row Count: 74,272

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	47814	`int(10) unsigned`	range
`chromEnd`	51482	`int(10) unsigned`	range
`name`	IRF_improved_6498_1	`varchar(255)`	values
`score`	231	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	47814	`int(10) unsigned`	range
`thickEnd`	51482	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	278,273	`longblob`
`chromStarts`	0,3395	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
585	improved_6498	47814	51482	IRF_improved_6498_1	231	+	47814	51482	0	2	278,273	0,3395
585	improved_6498	47955	54698	IRF_improved_6498_4	395	+	47955	54698	0	2	443,448	0,6295
585	improved_6498	48562	51531	IRF_improved_6498_0	243	+	48562	51531	0	2	352,305	0,2664
585	improved_6498	48562	51531	IRF_improved_6498_2	293	+	48562	51531	0	2	179,179	0,2790
585	improved_6498	48794	54698	IRF_improved_6498_5	202	+	48794	54698	0	2	166,182	0,5722
585	improved_6498	52616	53091	IRF_improved_6498_3	46	+	52616	53091	0	2	75,77	0,398
585	improved_6498	53905	59109	IRF_improved_6498_8	217	+	53905	59109	0	2	251,221	0,4983
585	improved_6498	53905	59109	IRF_improved_6498_9	270	+	53905	59109	0	2	205,215	0,4989
585	improved_6498	54081	58989	IRF_improved_6498_7	122	+	54081	58989	0	2	101,101	0,4807
585	improved_6498	54107	58989	IRF_improved_6498_10	127	+	54107	58989	0	2	101,101	0,4781

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

Inverted Repeats (irf) Track Description


	Description Inverted repeats within each scaffold of the D. mojavensis genome is identified using Inverted Repeats Finder with the following parameters: Match: 2 Mismatch: 3 Delta: 5 Match Probability: 80 Indel Probability: 10 Min Score: 40 Max Length: 10000 Max Loop: 50000 t4: 74 t5: 493 t7: 5000 References P. E. Warburton, J. Giordano, F. Cheung, Y. Gelfand and G. Benson. Inverted Repeat Structure of the Human Genome: The X-Chromosome Contains a Preponderance of Large, Highly Homologous Inverted Repeats That Contain Testes Genes. Genome Research, 14:1861-1869, 2004.