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: dm6 Primary Table: irf Data last updated: 2016-01-23
Big Bed File: /gbdb/dm6/bbi/dm6_irf.bb
Item Count: 15,561
Format description: Browser Extensible Data

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15667731	Start position in chromosome
`chromEnd`	15702761	End position in chromosome
`name`	IRF_chr2L_284	Name of item.
`score`	44	Score (0-1000)
`strand`	+	+ or - for strand
`thickStart`	15667731	Start of where display should be thick (start codon)
`thickEnd`	15702761	End of where display should be thick (stop codon)
`reserved`	0,0,0	Used as itemRgb as of 2004-11-22
`blockCount`	2	Number of blocks
`blockSizes`	33,33	Comma separated list of block sizes
`chromStarts`	0,34997	Start positions relative to chromStart

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
chr2L	15667731	15702761	IRF_chr2L_284	44	+	15667731	15702761	0,0,0	2	33,33	0,34997
chr2L	15838498	15838750	IRF_chr2L_285	40	+	15838498	15838750	0,0,0	2	20,20	0,232
chr2L	15905350	15913244	IRF_chr2L_286	51	+	15905350	15913244	0,0,0	2	33,33	0,7861
chr2L	15955138	15955323	IRF_chr2L_287	43	+	15955138	15955323	0,0,0	2	48,45	0,140
chr2L	16229769	16229970	IRF_chr2L_288	56	+	16229769	16229970	0,0,0	2	38,38	0,163
chr2L	16239995	16276301	IRF_chr2L_290	58	+	16239995	16276301	0,0,0	2	34,34	0,36272
chr2L	16276241	16276301	IRF_chr2L_289	50	+	16276241	16276301	0,0,0	2	30,30	0,30
chr2L	16365352	16365481	IRF_chr2L_291	42	+	16365352	16365481	0,0,0	2	21,21	0,108
chr2L	16479652	16513113	IRF_chr2L_294	44	+	16479652	16513113	0,0,0	2	68,67	0,33394
chr2L	16479681	16513418	IRF_chr2L_295	53	+	16479681	16513418	0,0,0	2	44,44	0,33693

Inverted Repeats (irf) Track Description


	Description Inverted repeats within each scaffold of the D. melanogaster 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: 50000 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.