Schema for Simple Repeats - Simple Tandem Repeats by TRF

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Schema for Simple Repeats - Simple Tandem Repeats by TRF

Database: DanaWGS Primary Table: simpleRepeat Row Count: 143,124

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	scaffold_0	`varchar(255)`	values
`chromStart`	410	`int(10) unsigned`	range
`chromEnd`	975	`int(10) unsigned`	range
`name`	trf	`varchar(255)`	values
`period`	189	`int(10) unsigned`	range
`copyNum`	3	`float`	range
`consensusSize`	189	`int(10) unsigned`	range
`perMatch`	96	`int(10) unsigned`	range
`perIndel`	0	`int(10) unsigned`	range
`score`	1015	`int(10) unsigned`	range
`A`	32	`int(10) unsigned`	range
`C`	16	`int(10) unsigned`	range
`G`	21	`int(10) unsigned`	range
`T`	29	`int(10) unsigned`	range
`entropy`	1.95	`float`	range
`sequence`	ATCTACAAATCGATTGAGGTATTCCGC...	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	period	copyNum	consensusSize	perMatch	perIndel	score	A	C	G	T	entropy	sequence
585	scaffold_0	410	975	trf	189	3	189	96	0	1015	32	16	21	29	1.95	ATCTACAAATCGATTGAGGTATTCCGCTTAAGAATCGGATGGAAATTGGCCAAGATATAGCCATCGCTGGGGGCCATATTGTCCTGCCATGCATTTTCTCAATTAATGAAGGGGACCCCCCAGAAATT ...
585	scaffold_0	902	1043	trf	73	1.9	73	94	0	246	39	14	17	29	1.88	CCCCCCAGAAAATTCGATGAAAAATCTAAAAAATATTTTGTTCCTAGATTTTGATGGAAAAGGATGGAGAATC
585	scaffold_1	0	1483	trf	189	7.9	189	95	1	2550	28	18	19	33	1.96	AAATCTAGGAACAAAATATTTTTGAGATTTTTTGTCAAAATTTCTGGGGGATCCCCTTCGAAATTATGAAAAGTGCATGGAAGGACAATATGGCCCCTAGCGATGGCTATATCTTGGCCAATTTCCAT ...
585	scaffold_10	6	4514	trf	188	24.3	188	87	3	6366	32	17	21	28	1.96	GATTTTTGGCAAAGATATAGCCTTGGCAGTGGGTCATATCGGGCACTCCTGCGTTTTCCAACATTTTGAAGGGGATCCCCCAGGAAATTTGACAAAAAATATAAAAAAAATAGTTTCCCAGATTTTGA ...
585	scaffold_10	6	4513	trf	367	12.2	368	90	3	6458	32	17	21	28	1.96	GATTTTTGGCAAAGATATAGCCTTGGCAGTGGGTCATATCGGGCACTCCTTCGTTTTCCAATATTTTGACGGGGATCCCCCAGGGAAAAAAATTTAAAAAAAAAATAGTTTCCCTGATTTTGATGCAG ...
585	scaffold_10000	307	436	trf	67	1.9	67	96	0	240	31	20	25	23	1.98	TGATCCTAACAGATGGCGTTCGCAGCTCCGAAAAGCTGACTCGGTGAATAGTGAACGAAATATCGTG
585	scaffold_10001	0	1208	trf	525	2.3	524	92	1	1985	25	18	22	33	1.96	CTAACAGTGAAGTTTTTCTAGCCGGTTTTATCGCCAAATTATTGATGATTTTCGAGTGGTTTTTTTTGCGATAACAGCGATGATTTTCTAGCCTTTTTTATCGACAAATTAGCGATGATTTTCTAGCG ...
585	scaffold_10001	323	686	trf	68	5.3	67	82	5	433	23	17	20	38	1.93	TAACAGTGATGATTTTCTAGCCGGTTTTATCGCAAATTAGCGATGATTTTCAAGCGGTTTTTAGCGC
585	scaffold_10001	323	686	trf	135	2.7	135	83	3	451	23	17	20	38	1.93	TAACAGTGATGATTTTCTAGCCGTTTTATCGCTAAATTAGCGATGATTTTCAAGCGGTTTTTAGCGCTAACAGTGATGATTTTCTAGCCGGTTTTATCGACAAATGAGCGATGATTTTCAAGCGGTTT ...
585	scaffold_10001	324	685	trf	35	10.6	34	71	11	238	23	17	20	38	1.93	AACAGCGATGATTTTCTAGCGGTTTTTATCGCTA

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.