Schema for Simple Repeats - Simple Tandem Repeats by TRF

Database: DhydGB1 Primary Table: simpleRepeat Row Count: 93,490 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	NWQH01000001	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	1346	`int(10) unsigned`	range
`name`	TATCTAATAACCAAAC	`varchar(255)`	values
`period`	51	`int(10) unsigned`	range
`copyNum`	26.4	`float`	range
`consensusSize`	50	`int(10) unsigned`	range
`perMatch`	71	`int(10) unsigned`	range
`perIndel`	5	`int(10) unsigned`	range
`score`	710	`int(10) unsigned`	range
`A`	46	`int(10) unsigned`	range
`C`	18	`int(10) unsigned`	range
`G`	7	`int(10) unsigned`	range
`T`	28	`int(10) unsigned`	range
`entropy`	1.75	`float`	range
`sequence`	TATCTAATAACCAAACCAATCCAATAA...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	period	copyNum	consensusSize	perMatch	perIndel	score	A	C	G	T	entropy	sequence
585	NWQH01000001	0	1346	TATCTAATAACCAAAC	51	26.4	50	71	5	710	46	18	7	28	1.75	TATCTAATAACCAAACCAATCCAATAAATAACCTATACAATAATTGGACT
585	NWQH01000001	0	4537	TATCTAATAACCGAAC	102	44.4	102	69	10	1049	46	18	7	27	1.75	TATCTAATAACCGAACCAATCCAATATATAAGCATATACAATAAGCAGACTTATCTAATATCCAAACCAATGCAATAAATTGACCAAAACAATAATTGGACT
585	NWQH01000001	35	6553	ATACAATAATTGGACT	153	42.4	153	74	9	2407	46	18	7	27	1.76	ATACAATAATTGGACTTATCTAATAACCGAACCAATCCAATATATAAGCATATACAATAAGTATACTTAGCCAATAACAGAACCAATTTAATAAATTAACATATACAATAATGGGACTTATCTAATAT ...
585	NWQH01000001	1440	6535	AATAACCGAACCAATT	51	99.4	51	69	9	1640	46	18	7	27	1.76	AATAACCGAACCAATTCAATAAATTAACATACACAATAATTGGACTTATCT
585	NWQH01000001	2102	2141	AATAAATAAACCAATA	17	2.3	17	86	0	51	58	15	2	23	1.49	AATAAATAAACCAATAC
585	NWQH01000001	9182	9493	AGAGCCCAAAGCTTTG	160	1.9	163	85	3	432	33	24	19	22	1.97	AGAGCCCAAAGCTTTGCTGTAGCCAAGCTCAGAACCCATAGTCAAGCACACAACCAAGCAATCAATGACACAAGCCGAATTGAAGCTTTAATCCAGAAAGCTGTTACCTAAGATTAGGCCCAGCAAGA ...
585	NWQH01000001	10791	10820	ACCTTACAATAATC	14	2.1	14	100	0	58	44	27	0	27	1.54	ACCTTACAATAATC
585	NWQH01000001	21635	21682	TA	2	23.5	2	95	0	85	48	2	0	48	1.13	TA
585	NWQH01000001	24944	24986	AATATTTAAAGTAGGC	20	2.1	20	86	0	57	50	4	16	28	1.66	AATATTTAAAGTAGGCAAGA
585	NWQH01000001	28379	28522	TGTG	4	35.8	4	75	0	97	2	11	46	39	1.55	TGTG

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

Description