Shannon entropy measures how unpredictable the base sequence is inside a window. A window of unique, random-looking sequence scores close to two bits per base, while a window filled with a short motif repeated over and over scores much lower. Dips in this track therefore mark simple repeats, satellite arrays and other low-complexity DNA, which is useful for reading the repeat tracks alongside it.
A bar graph with one value per 200 bp window, autoscaled to the data in view. Values run from 0 to about 2 bits per base.
Shannon entropy was computed with Teloscope over the same non-overlapping 200 bp windows as the GC track (-w 200 -s 200) with the -e flag. See vgl-hub/teloscope for the tool and the manuscript for the full parameters.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/general/bTaeGut7v0.4_MT_rDNA.Teloscope.entropy.bw. It is already in a binary indexed format that the browser reads over the network, so the track points at it where it is and no copy is kept in the hub. The 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=seqEntropy.
This track points straight at the file on GenomeArk rather than at a copy in the hub, so no download step is needed to work with it: bigWigToBedGraph reads it over the network, as does the browser.
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.