Schema for Simple Repeats - Simple Tandem Repeats by TRF

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Schema for Simple Repeats - Simple Tandem Repeats by TRF

Database: DkikGB2 Primary Table: simpleRepeat Row Count: 58,125

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFH02000012	`varchar(255)`	values
`chromStart`	0	`int(10) unsigned`	range
`chromEnd`	36	`int(10) unsigned`	range
`name`	trf	`varchar(255)`	values
`period`	16	`int(10) unsigned`	range
`copyNum`	2.2	`float`	range
`consensusSize`	16	`int(10) unsigned`	range
`perMatch`	90	`int(10) unsigned`	range
`perIndel`	5	`int(10) unsigned`	range
`score`	54	`int(10) unsigned`	range
`A`	13	`int(10) unsigned`	range
`C`	5	`int(10) unsigned`	range
`G`	2	`int(10) unsigned`	range
`T`	77	`int(10) unsigned`	range
`entropy`	1.05	`float`	range
`sequence`	TTTTCAATTATTTTTT	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	period	copyNum	consensusSize	perMatch	perIndel	score	A	C	G	T	entropy	sequence
585	AFFH02000012	0	36	trf	16	2.2	16	90	5	54	13	5	2	77	1.05	TTTTCAATTATTTTTT
585	AFFH02000012	25	198	trf	89	1.9	89	95	4	314	17	19	13	49	1.79	TATTTTTTTTTATTTAACTGCCCTCTGACTTTTTGTCAGCTTAGTTTGTGGCTAACTGCCTCTGATCTTTGTCAGATAATTCTTTTCAC
585	AFFH02000023	236	275	trf	8	4.9	8	93	0	69	35	25	38	0	1.56	ACGGACAG
585	AFFH02000023	629	666	trf	14	2.4	16	78	17	51	43	10	2	43	1.53	TATATATTTACAATAC
585	AFFH02000023	634	664	trf	14	2.1	14	100	0	60	43	13	0	43	1.43	ATTTACAATACTAT
585	AFFH02000038	1056	1207	trf	63	2.4	63	98	0	293	28	23	19	28	1.98	AGACCTGATCTGTTTACCAGGTCTGATAAACCGTATCAGGTCTGATAAACCGACCTGATAATC
585	AFFH02000038	1207	1443	trf	120	1.9	121	88	8	354	36	10	5	47	1.61	TTTTCATTTTTTAACTGAAATATAAAGGCTGAAAAAAAAATATTTCCCAAGTCCCTTTTCCCAATAAAAAATTTGTAATATTTTTATAATATAAAATTTTTTTATTAATTATTATTTTTTT
585	AFFH02000038	1410	1450	trf	18	2.1	18	86	13	53	35	0	2	62	1.09	TTTTTATAATATTAAATT
585	AFFH02000038	1792	1876	trf	9	9.3	9	77	12	84	13	11	52	22	1.72	TGGAGCTGG
585	AFFH02000038	1900	1938	trf	15	2.5	15	86	0	58	2	21	34	42	1.67	TGCTGCTGTTGCTGC

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