Schema for Simple Repeats - Simple Tandem Repeats by TRF

Database: DsimGB2 Primary Table: simpleRepeat Row Count: 27,840 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	CM002910	`varchar(255)`	values
`chromStart`	2285	`int(10) unsigned`	range
`chromEnd`	2466	`int(10) unsigned`	range
`name`	AAATTAGATTTTAACG	`varchar(255)`	values
`period`	31	`int(10) unsigned`	range
`copyNum`	5.8	`float`	range
`consensusSize`	31	`int(10) unsigned`	range
`perMatch`	79	`int(10) unsigned`	range
`perIndel`	8	`int(10) unsigned`	range
`score`	179	`int(10) unsigned`	range
`A`	28	`int(10) unsigned`	range
`C`	19	`int(10) unsigned`	range
`G`	8	`int(10) unsigned`	range
`T`	43	`int(10) unsigned`	range
`entropy`	1.8	`float`	range
`sequence`	AAATTAGATTTTAACGTTTGCCCATCC...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	period	copyNum	consensusSize	perMatch	perIndel	score	A	C	G	T	entropy	sequence
585	CM002910	2285	2466	AAATTAGATTTTAACG	31	5.8	31	79	8	179	28	19	8	43	1.8	AAATTAGATTTTAACGTTTGCCCATCCTTCA
585	CM002910	2629	2717	AAAATCTAATTTAAAG	31	2.8	30	85	10	115	43	9	22	25	1.82	AAAATCTAATTTAAAGGGTGGGCAAACGTT
585	CM002910	2698	2815	AATTTTAAAGGATGGG	61	1.9	62	89	1	182	42	7	22	27	1.8	AATTTTAAAGGATGGGCAAACGAAATTATTTAGTTTTAAGAGGTGAACAAACGAAAAAAACG
585	CM002910	2699	2823	ATTTTTAAGGGTGGGC	31	4.1	30	71	3	113	41	7	20	30	1.8	ATTTTTAAGGGTGGGCAAACGAAATTATTT
585	CM002910	5119	5454	TTAAAATTGGCTTTCT	175	1.9	175	88	2	512	22	15	17	44	1.86	TTAAAATTGGCTTTCTTCGGGCGCTGTTTTTGGCGTTCCTACTTTGCTGCCTCCGTTCGATTTTTCGTGAGATATTTTCGTAATTATAGATTTAATTACAACAGAACTAGTACTCGTTTCCGTCGTAT ...
585	CM002910	16597	16629	TTACATTTTATTG	14	2.4	13	94	5	55	28	9	6	56	1.55	TTACATTTTATTG
585	CM002910	21265	21297	ATTGTTTGATAGAAT	16	2.1	15	94	5	55	37	0	18	43	1.51	ATTGTTTGATAGAAT
585	CM002910	38949	38986	ATATATTAA	9	4	9	93	6	65	56	0	0	43	0.99	ATATATTAA
585	CM002910	52410	52441	ATATGTATGCATGTAC	16	1.9	16	93	0	53	32	6	19	41	1.77	ATATGTATGCATGTAC
585	CM002910	59050	59159	TTTTAAACGAGTTGTG	35	3.2	35	69	8	91	26	13	21	38	1.91	TTTTAAACGAGTTGTGTATAGTGACTTCACTGCGA

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