Schema for Simple Repeats - Simple Tandem Repeats by TRF

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Schema for Simple Repeats - Simple Tandem Repeats by TRF

Database: DsuzGB1 Primary Table: simpleRepeat Row Count: 53,450

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AWUT01012676	`varchar(255)`	values
`chromStart`	5995	`int(10) unsigned`	range
`chromEnd`	6024	`int(10) unsigned`	range
`name`	trf	`varchar(255)`	values
`period`	11	`int(10) unsigned`	range
`copyNum`	2.5	`float`	range
`consensusSize`	12	`int(10) unsigned`	range
`perMatch`	94	`int(10) unsigned`	range
`perIndel`	5	`int(10) unsigned`	range
`score`	51	`int(10) unsigned`	range
`A`	31	`int(10) unsigned`	range
`C`	0	`int(10) unsigned`	range
`G`	17	`int(10) unsigned`	range
`T`	51	`int(10) unsigned`	range
`entropy`	1.45	`float`	range
`sequence`	GTATTATGTAAT	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	period	copyNum	consensusSize	perMatch	perIndel	score	A	C	G	T	entropy	sequence
585	AWUT01012676	5995	6024	trf	11	2.5	12	94	5	51	31	0	17	51	1.45	GTATTATGTAAT
585	AWUT01012676	14724	14985	trf	128	2	127	83	5	321	24	13	27	34	1.93	TGGGCGTTAGAGTGGGCGTGGCAACTTTTTTTGGATCAATCGATAGGTATTGAAGAAAACAATACATTTCAGTTGAAATTTTTGTTCTACCATCAAAAATGTAGAAGCCACAGGTTTGGGCGGTTTG
585	AWUT01012676	19135	19172	trf	18	2.1	18	94	0	65	16	29	18	35	1.93	TTATGCCAGACCTTCTGC
585	AWUT01012676	35751	36012	trf	119	2.2	119	95	0	468	23	13	29	33	1.93	TGGGCGTTAGAGTGGGCGTGGCAAACTTTTTTTGGATCAATCGATAGGTATTGACGAGACCAATACACTTCAGTTAAAATTTTTTATCTAGCATGAAACTTGTGGGCTTGGGCGGTTTG
585	AWUT01012676	41295	41712	trf	163	2.6	163	92	0	681	36	14	13	35	1.85	ATAAAATTAAATTTGAAATTCAGAACTAATTAAAAAATGTTATTTCCAAGCGTAGGAGGTTATATGTTAAAAAACACCGAAGCTATAATTTGTTTCATATTATTTTCCAACCAATTTTCCGATCGTTC ...
585	AWUT01012676	43528	43709	trf	95	1.9	95	87	3	267	27	14	24	32	1.95	TCGATAGGTATTGACGAGACCAAAACATTTAGGTAACAACTTTTTATCTAGCATGAAAAGTGTGGGCGCCACAGGCTTGGGCGGTTTTAGATCAT
585	AWUT01012676	48719	51247	trf	1264	2	1264	100	0	5056	29	23	20	26	1.99	AATAAAGGTGGATAAACCTGTTGGATGATTTAAAGAACCTAGCGAACATTCAAATACCTCGATTTGTATACACCTCCGACTCGCATCACAGTGAAATACATGGCTCCGCTGACACATCTGAAGAACAT ...
585	AWUT01012676	65683	65871	trf	18	10.4	18	89	0	286	48	21	1	28	1.59	TACATACATACAAATATC
585	AWUT01012676	66460	66488	trf	8	3.5	8	100	0	56	0	35	25	39	1.56	TGTCCGTC
585	AWUT01012676	72755	72795	trf	21	1.9	21	89	0	62	27	42	15	15	1.86	CTCAGCCGACATAAACGCCTC

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