Schema for Simple Repeats - Simple Tandem Repeats by TRF

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Schema for Simple Repeats - Simple Tandem Repeats by TRF

Database: dm6 Primary Table: simpleRepeat Row Count: 34,750

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	5204	`int(10) unsigned`	range
`name`	CGACAATGCACGACAG	`varchar(255)`	values
`period`	458	`int(10) unsigned`	range
`copyNum`	11.4	`float`	range
`consensusSize`	458	`int(10) unsigned`	range
`perMatch`	99	`int(10) unsigned`	range
`perIndel`	0	`int(10) unsigned`	range
`score`	10363	`int(10) unsigned`	range
`A`	31	`int(10) unsigned`	range
`C`	19	`int(10) unsigned`	range
`G`	20	`int(10) unsigned`	range
`T`	28	`int(10) unsigned`	range
`entropy`	1.97	`float`	range
`sequence`	CGACAATGCACGACAGAGGAAGCAGAA...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	period	copyNum	consensusSize	perMatch	perIndel	score	A	C	G	T	entropy	sequence
585	chr2L	0	5204	CGACAATGCACGACAG	458	11.4	458	99	0	10363	31	19	20	28	1.97	CGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGGGAGAAATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCTCTTTGATTTTTT ...
585	chr2L	224	503	ATATGATCGCGTATGC	147	2	137	84	11	357	31	21	20	26	1.98	ATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCCATAATGACTGCCTCTCATTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGGAAGCAGAACAGATATTTAGATT ...
585	chr2L	682	961	ATATGATCGCGTATGC	147	2	137	84	11	357	31	21	20	26	1.98	ATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCCATAATGACTGCCTCTCATTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGGAAGCAGAACAGATATTTAGATT ...
585	chr2L	1140	1419	ATATGATCGCGTATGC	147	2	137	84	11	357	31	21	20	26	1.98	ATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCCATAATGACTGCCTCTCATTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGGAAGCAGAACAGATATTTAGATT ...
585	chr2L	1598	1877	ATATGATCGCGTATGC	147	2	137	84	11	357	31	21	20	26	1.98	ATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCCATAATGACTGCCTCTCATTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGGAAGCAGAACAGATATTTAGATT ...
585	chr2L	2056	2335	ATATGATCGCGTATGC	147	2	137	84	11	357	31	21	20	26	1.98	ATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCCATAATGACTGCCTCTCATTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGGAAGCAGAACAGATATTTAGATT ...
585	chr2L	2514	2793	ATATGATCGCGTATGC	147	2	137	84	11	357	31	21	20	26	1.98	ATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCCATAATGACTGCCTCTCATTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGGAAGCAGAACAGATATTTAGATT ...
585	chr2L	2972	3251	ATATGATCGCGTATGC	147	2	137	84	11	357	31	21	20	26	1.98	ATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCCATAATGACTGCCTCTCATTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGGAAGCAGAACAGATATTTAGATT ...
585	chr2L	3430	3709	ATATGATCGCGTATGC	147	2	137	84	11	357	31	21	20	26	1.98	ATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCCATAATGACTGCCTCTCATTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGGAAGCAGAACAGATATTTAGATT ...
585	chr2L	3888	4167	ATATGATCGCGTATGC	147	2	137	84	11	357	31	21	20	26	1.98	ATATGATCGCGTATGCGAGAGTAGTGCCAACATATTGTGCCATAATGACTGCCTCTCATTCTGTCTTATATTACCGCAAACCCAAAAAGACAATACACGACAGAGGAAGCAGAACAGATATTTAGATT ...

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

Simple Repeats (simpleRepeat) Track Description


	Description This track displays simple tandem repeats (possibly imperfect repeats) located by Tandem Repeats Finder (TRF) which is specialized for this purpose. These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases. Methods For more information about the TRF program, see Benson (1999). Credits TRF was written by Gary Benson. References Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80. PMID: 9862982; PMC: PMC148217