Schema for Simple Repeats - Simple Tandem Repeats by TRF

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Schema for Simple Repeats - Simple Tandem Repeats by TRF

Database: DbipGB2 Primary Table: simpleRepeat Row Count: 49,174

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	AFFE02000007	`varchar(255)`	values
`chromStart`	46	`int(10) unsigned`	range
`chromEnd`	88	`int(10) unsigned`	range
`name`	trf	`varchar(255)`	values
`period`	21	`int(10) unsigned`	range
`copyNum`	2	`float`	range
`consensusSize`	22	`int(10) unsigned`	range
`perMatch`	95	`int(10) unsigned`	range
`perIndel`	4	`int(10) unsigned`	range
`score`	77	`int(10) unsigned`	range
`A`	66	`int(10) unsigned`	range
`C`	4	`int(10) unsigned`	range
`G`	4	`int(10) unsigned`	range
`T`	23	`int(10) unsigned`	range
`entropy`	1.3	`float`	range
`sequence`	AAAAATAAGAAAAAAATTTCTA	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	period	copyNum	consensusSize	perMatch	perIndel	score	A	C	G	T	entropy	sequence
585	AFFE02000007	46	88	trf	21	2	22	95	4	77	66	4	4	23	1.3	AAAAATAAGAAAAAAATTTCTA
585	AFFE02000007	315	344	trf	11	2.7	11	94	5	51	27	10	0	62	1.28	TTTACATTATT
585	AFFE02000023	161	186	trf	1	25	1	100	0	50	100	0	0	0	0	A
585	AFFE02000025	77	259	trf	79	2.3	79	79	8	192	21	35	19	22	1.96	AGTGCCTAGCCGATTCCCCTGCCACCTGATAACCCGTCAATAAATGATATGCCTGCCCAATCTCCCTGCCAAGACCTGG
585	AFFE02000025	365	642	trf	142	2	142	81	2	324	19	35	28	16	1.94	TGCCGACGCATGCAAGGCCTGGCCAATCCCCTGCCAGCCGATAAACCACCAATACGTGAAGTGCCTAGCCGATCTAACTGCCAAGACCTGGAACGCCCCACCGATCACCCTGCCGAGGCGTAGAGTGC ...
585	AFFE02000025	640	1016	trf	190	2	188	85	3	513	20	34	22	22	1.97	CGATTCCCCTGCCACCTGATAACCCGTCAATAAATGATATGCCTGCCCGATCTCCCTGCCAAGACCGGGAGTGCCAAGCCGATTCCCAGCCAGTTGATAGCCCGCCAATACGTGAAAAACTGGCCAAT ...
585	AFFE02000025	960	1043	trf	32	2.6	32	88	0	112	18	36	24	21	1.95	CCCTGCCAAGGCCTGGAGTTCCCGCACGATTC
585	AFFE02000026	2197	2758	trf	126	4.4	126	88	0	834	26	24	33	16	1.96	GAGGAGCGGCGACAAGAGCAGGTGCAAAATACTGCTGACCATGCGACGCGGAGGACTATTCCGGAGTACCGAAATCCGGAACGGGTTCGGGACGCCACAGCGCGTGCTATTCGTCGAGAGGACTCC
585	AFFE02000043	7	1055	trf	359	2.9	360	91	3	1641	24	23	16	35	1.95	CCACAGTGATGGTCATATCTTTCCCAATTCTCATCCGATTCTCAAGCGGAGTACCTTAAATGATTTCTGGATCGATTCTCCACCATTCTGCATCAAAATCCTGAGACAAAATATTTTTTAGATTTTTT ...
585	AFFE02000043	21	1055	trf	180	5.7	181	90	3	1574	24	22	17	35	1.95	ATATCTTTCCCAATTCTCATCCGATTCTCAAGCGGAGTACCTTAAACGATTTCTGGATCGATTCTGCCACCATTCTGCATCAAAATCCTGAGACAAAATATTTTTTAGATTTTTTGTCCATTTTTCGT ...

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