This track is part of the Centromeres and Telomeres collection of the zebra finch telomere-to-telomere hub.
Interstitial telomeric sequences are stretches of the telomere motif found away from the chromosome ends. They are usually read as scars of ancient chromosome fusions or of repair at double-strand breaks, and they are fragile sites where further rearrangement tends to happen. This track shows 664 such clusters.
Each item is one cluster of telomeric repeat away from a chromosome end.
Telomeric blocks called by Teloscope were clustered with bedtools merge -d 200 and then filtered on TTAGGG repeat density, keeping clusters above 0.5. The resulting coordinates were classified by length and chromosomal position following the published scheme, and clusters above 5 kb were compared with the terminal telomeres using StainedGlass v0.6 at a 400 bp window.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/telomeres/bTaeGut7v0.4_MT_rDNA.teloscope.v0.3.its.merged200.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=itsRepeats.
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/itsRepeats.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
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.