This track is part of the Centromeres and Telomeres collection of the zebra finch telomere-to-telomere hub.
Telomeres are arrays of the motif TTAGGG that cap each chromosome end and protect it from being treated as a broken chromosome. An assembly that reaches the telomere on both ends of a chromosome is telomere-to-telomere for that chromosome, which is what this track lets you check. It contains 160 terminal telomere arrays.
Each item is one terminal telomere array, labelled p or q for the chromosome end it caps. The details page carries the array length and the counts of canonical and non-canonical repeat units.
Telomeres were annotated with Teloscope (-w 200 -s 200 -c TTAGGG -p NNNGGG -d 200 -l 500, with the flags -r -g -e -m -i) and with seqtk v1.4 run with -d 50000 to raise the maximum drop cutoff and recover additional telomeres. Contigs were then classified into eight categories by telomere completeness and gap presence.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/telomeres/bTaeGut7v0.4_MT_rDNA.Teloscope.terminal.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=telomeres.
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/telomeres.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.