Schema for Simple Repeats - Simple Tandem Repeats by TRF

Database: DbusGB1 Primary Table: simpleRepeat Row Count: 54,430 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CP012523	`varchar(255)`	values
`chromStart`	2611	`int(10) unsigned`	range
`chromEnd`	2651	`int(10) unsigned`	range
`name`	TGTTGC	`varchar(255)`	values
`period`	6	`int(10) unsigned`	range
`copyNum`	6.7	`float`	range
`consensusSize`	6	`int(10) unsigned`	range
`perMatch`	94	`int(10) unsigned`	range
`perIndel`	0	`int(10) unsigned`	range
`score`	62	`int(10) unsigned`	range
`A`	0	`int(10) unsigned`	range
`C`	20	`int(10) unsigned`	range
`G`	32	`int(10) unsigned`	range
`T`	47	`int(10) unsigned`	range
`entropy`	1.5	`float`	range
`sequence`	TGTTGC	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	period	copyNum	consensusSize	perMatch	perIndel	score	A	C	G	T	entropy	sequence
585	CP012523	2611	2651	TGTTGC	6	6.7	6	94	0	62	0	20	32	47	1.5	TGTTGC
585	CP012523	12755	12794	CAATTG	6	6.5	6	90	0	51	30	25	15	28	1.96	CAATTG
585	CP012523	15879	15914	CAG	3	11.7	3	87	0	52	31	37	28	2	1.72	CAG
585	CP012523	16867	16900	TGTGTGTGTGCTTTGT	16	2	17	94	5	59	0	3	36	60	1.12	TGTGTGTGTGCTTTGTT
585	CP012523	17704	17745	GTGTTTGGGGCCAGTG	19	2.2	19	86	0	55	2	14	43	39	1.59	GTGTTTGGGGCCAGTGGCT
585	CP012523	18803	18829	CACACAAGCA	10	2.6	10	100	0	52	50	42	7	0	1.31	CACACAAGCA
585	CP012523	22043	22074	AGACAGGC	8	3.9	8	91	0	53	41	22	35	0	1.54	AGACAGGC
585	CP012523	23727	23755	CAGC	4	7	4	100	0	56	25	50	25	0	1.5	CAGC
585	CP012523	29854	29880	CAG	3	8.7	3	100	0	52	34	34	30	0	1.58	CAG
585	CP012523	31839	31872	GCCGCT	6	5.5	6	92	0	57	3	51	33	12	1.54	GCCGCT

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