This track is part of the Repeats collection of the zebra finch telomere-to-telomere hub.
A tandem repeat is a short motif repeated directly head to tail, from a few bases up to arrays spanning megabases. They mutate quickly by slippage during replication, they are the basis of many genetic markers, and long arrays of them are what makes centromeric and subtelomeric DNA so difficult to assemble. This track shows about 980,000 tandem repeat arrays across both euchromatin and heterochromatin.
Each array is drawn as a single feature named after its repeat unit. The repeat unit and the full array sequence are kept as extra fields on the details page. Item names longer than 255 characters are truncated for display; the untruncated repeat unit is in the extra fields. The track is set to dense by default because of the number of arrays.
Tandem repeats were called de novo across the assembly with Tandem Repeats Finder. In the manuscript, TRF is used to extract monomer units from satellite arrays for the comparison of Tgut191A-like repeats across bird genomes; the genome-wide call set distributed with the assembly is what is shown here.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/repeats/bTaeGut7v0.4_MT_rDNA.trf.sorted.v0.1.bed. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. The conversion, and the whole hub, is reproduced by the commands in src/hg/makeDb/doc/contrib/bTaeGut7.txt of the UCSC kent source tree.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=tandemRepeats.
For automated download and analysis, this annotation is a bigBed file inside the hub. Individual regions or the whole annotation can be obtained with bigBedToBed, which can be compiled from source or downloaded as a precompiled binary; instructions are here. The tool also fetches a range, for example bigBedToBed <hubUrl>/GCF_048771995.1/tandemRepeats.bb -chrom=NC_133024.1 -start=0 -end=100000 stdout, where <hubUrl> is the directory this hub was loaded from.
The original annotation files are on GenomeArk, in the bTaeGut7 annotations directory.
Formenti G, Jain N, Medico JA, Sollitto M, Antipov D, Barcellos S, Biegler M, Borges I, Chang JK, Chen Y et al. The complete genome of a songbird. Cell. 2026 Aug 6;189(16):4922-4945.e12. PMID: 42561917
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
The assembly and all of these annotations were produced by the Vertebrate Genome Laboratory at The Rockefeller University and their collaborators, and released through GenomeArk. Thanks to Giulio Formenti and Erich D. Jarvis and their co-authors for making the data available before and after publication. The analysis code is at github.com/gf777/T2T-zebra-finch. This hub was assembled at UCSC from the IGV session distributed with the annotations, using hubtools.