Schema for Simple Repeats - Simple Tandem Repeats by TRF
  Database: hub_567047_hs1    Primary Table: hub_567047_simpleRepeat Data last updated: 2022-02-06
Big Bed File Download: /gbdb/hs1/bbi/simpleRepeat.bb
Item Count: 1,155,353
The data is stored in the binary BigBed format.

Format description: Describes the Simple Tandem Repeats
fieldexampledescription
chromCP068255.2Reference sequence chromosome or scaffold
chromStart102846470Start position in chromosome
chromEnd102846498End position in chromosome
nameASimple Repeats tag name
period1Length of repeat unit
copyNum28.0Mean number of copies of repeat
consensusSize1Length of consensus sequence
perMatch100Percentage Match
perIndel0Percentage Indel
score56Alignment Score = 2*match-7*mismatch-7*indel; minscore=50
A100Percent of A's in repeat unit
C0Percent of C's in repeat unit
G0Percent of G's in repeat unit
T0Percent of T's in repeat unit
entropy0.00Entropy
sequenceASequence of repeat unit element

Sample Rows
 
chromchromStartchromEndnameperiodcopyNumconsensusSizeperMatchperIndelscoreACGTentropysequence
CP068255.2102846470102846498A128.011000561000000.00A
CP068255.2102847599102847630AATAAATAAT103.010909536700320.91AATAAATAAT
CP068255.2102848502102848568AATAAAAAATAAAAAA302.230895988300160.65AATAAAAAATAAAAAAATAAAAAAATAAAA
CP068255.2102848507102848568AAAAAAT78.478910888300160.64AAAAAAT
CP068255.2102848516102848568AAAT413.848411748200170.66AAAT
CP068255.2102852790102852870ATTATAATTAATATAT312.7308312875003461.19ATTATAATTAATATATAATTATAATAAGTG
CP068255.2102852831102852869ATATATAATTATAAAT192.019940675500440.99ATATATAATTATAAATAAT
CP068255.2102859277102859305TA214.021000565000501.00TA
CP068255.2102878077102878113CATCAGGGCA103.71092765273030111.91CATCAGGGCA
CP068255.2102881222102881247T125.011000500001000.00T

Simple Repeats (hub_567047_simpleRepeat) Track Description
 

Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 24 Jan 2022 Homo sapiens/GCA_009914755.4_T2T-CHM13v2.0/GCA_009914755.4 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 1,155,353 items in the track covering 277,065,041 bases, assembly size 3,117,292,070 bases, percent coverage % 8.89.

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