Schema for Simple Repeats - Simple Tandem Repeats by TRF

Database: hub_32_GCF_009829145.1 Primary Table: hub_32_simpleRepeat Data last updated: 2022-12-19
Big Bed File: https://hgdownload.soe.ucsc.edu/hubs/GCF/009/829/145/GCF_009829145.1/bbi/GCF_009829145.1_bChiLan1.pri.simpleRepeat.bb
Item Count: 247,189
Format description: Describes the Simple Tandem Repeats

field	example	description
`chrom`	NC_045637.1	Reference sequence chromosome or scaffold
`chromStart`	104232931	Start position in chromosome
`chromEnd`	104233067	End position in chromosome
`name`	GGAGG	Simple Repeats tag name
`period`	5	Length of repeat unit
`copyNum`	27.2	Mean number of copies of repeat
`consensusSize`	5	Length of consensus sequence
`perMatch`	100	Percentage Match
`perIndel`	0	Percentage Indel
`score`	272	Alignment Score = 2match-7mismatch-7*indel; minscore=50
`A`	19	Percent of A's in repeat unit
`C`	0	Percent of C's in repeat unit
`G`	80	Percent of G's in repeat unit
`T`	0	Percent of T's in repeat unit
`entropy`	0.72	Entropy
`sequence`	GGAGG	Sequence of repeat unit element

Sample Rows

chrom	chromStart	chromEnd	name	period	copyNum	consensusSize	perMatch	perIndel	score	A	C	G	T	entropy	sequence
NC_045637.1	104232931	104233067	GGAGG	5	27.2	5	100	0	272	19	0	80	0	0.72	GGAGG
NC_045637.1	104238205	104238264	TTCCA	5	11.8	5	100	0	118	18	40	0	40	1.51	TTCCA
NC_045637.1	104241193	104241234	AAAGTGAAAAAATGTA	19	2.2	19	95	0	73	63	2	19	14	1.41	AAAGTGAAAAAATGTAGAA
NC_045637.1	104244028	104244083	T	1	55.0	1	88	0	83	0	5	0	94	0.31	T
NC_045637.1	104244031	104244083	TTTTTTTTTTC	11	4.8	11	97	2	97	0	5	0	94	0.32	TTTTTTTTTTC
NC_045637.1	104264181	104264222	TTTGGTTTGGTTT	13	3.2	13	86	6	57	0	2	26	70	0.99	TTTGGTTTGGTTT
NC_045637.1	104270591	104270624	TAGCAGCAATATTAGT	17	1.9	17	93	0	57	33	12	21	33	1.90	TAGCAGCAATATTAGTT
NC_045637.1	104325309	104325377	TGTTTT	6	11.7	6	79	6	59	0	0	16	83	0.64	TGTTTT
NC_045637.1	104325312	104325357	TTTTGTTTTTTTGTGG	16	2.8	16	86	10	56	0	0	20	80	0.72	TTTTGTTTTTTTGTGG
NC_045637.1	104325346	104325374	T	1	28.0	1	100	0	56	0	0	0	100	0.00	T

Simple Repeats (hub_32_simpleRepeat) Track Description


	Description This track displays simple tandem repeats (possibly imperfect repeats) on the 03 Jan 2020 Chiroxiphia lanceolata/GCF_009829145.1_bChiLan1.pri/GCF_009829145.1 genome assembly, 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. There are 247,189 items in the track covering 17,825,287 bases, assembly size 1,089,631,598 bases, percent coverage % 1.64. 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 Credits This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished). References Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447

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