Schema for Simple Repeats - Simple Tandem Repeats by TRF

Schema for Simple Repeats - Simple Tandem Repeats by TRF

Database: bosTau4 Primary Table: simpleRepeat Row Count: 441,972
Format description: Describes the Simple Tandem Repeats

field	example	SQL type	info	description
`bin`	585	`smallint unsigned`	range	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`chromStart`	1978	`int unsigned`	range	Start position in chromosome
`chromEnd`	2009	`int unsigned`	range	End position in chromosome
`name`	trf	`varchar(255)`	values	Simple Repeats tag name
`period`	2	`int unsigned`	range	Length of repeat unit
`copyNum`	15.5	`float`	range	Mean number of copies of repeat
`consensusSize`	2	`int unsigned`	range	Length of consensus sequence
`perMatch`	100	`int unsigned`	range	Percentage Match
`perIndel`	0	`int unsigned`	range	Percentage Indel
`score`	62	`int unsigned`	range	Score between and . Best is .
`A`	48	`int unsigned`	range	Percent of A's in repeat unit
`C`	51	`int unsigned`	range	Percent of C's in repeat unit
`G`	0	`int unsigned`	range	Percent of G's in repeat unit
`T`	0	`int unsigned`	range	Percent of T's in repeat unit
`entropy`	1	`float`	range	Entropy
`sequence`	CA	`longblob`		Sequence of repeat unit element

Sample Rows

bin	chrom	chromStart	chromEnd	name	period	copyNum	consensusSize	perMatch	perIndel	score	A	C	G	T	entropy	sequence
585	chr1	1978	2009	trf	2	15.5	2	100	0	62	48	51	0	0	1	CA
585	chr1	9625	9885	trf	143	1.8	144	81	2	326	24	24	29	21	1.99	GGAGAAGGAAATGGCAACCCACTCCAGTACTCTTGCCTAGAAAATCCCAGGGACGGAGGAGCCTAGAAGGCTGCAGTCCATGGGGTCACACAGAGTCGGACACAACTGAAGTGACTTCACTTTCACTT ...
585	chr1	13442	13558	trf	44	2.6	44	97	0	214	56	7	9	26	1.59	TTCAAGAAAAGTAAACATTTAAATTGATAACAAAATATAAGAAA
585	chr1	14297	14875	trf	5	115.8	5	67	20	191	45	3	1	49	1.25	ATATT
585	chr1	14297	14914	trf	2	344	2	65	25	253	46	3	1	49	1.26	AT
585	chr1	14301	14896	trf	7	84.4	7	69	17	240	46	3	1	49	1.25	TATATTA
585	chr1	14362	14896	trf	87	6.5	82	67	20	79	46	3	1	49	1.25	TATATTATATATATATATTATATATAATATACAATATATTTACATATTATTATATATATTATATATAATATATAATAATATA
585	chr1	16414	16956	trf	2	292	2	65	20	196	43	2	2	51	1.28	AT
585	chr1	16416	16515	trf	37	2.7	36	80	9	112	46	2	3	48	1.29	ATATATAATATATTATATTAATATATTATGATATTA
585	chr1	16541	16869	trf	87	3.7	89	77	11	279	41	2	2	54	1.24	ATATATAATTATATATTTTATATATCATATATTTATTATATATTATATATTTATATATATATATATTTATATATTTAAATTATATATTT

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) 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.