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    Area of Science:

    • Genomics
    • Bioinformatics
    • Computational Biology

    Background:

    • Zimin words are defined as patterns with identical prefixes and suffixes.
    • These unavoidable patterns occur in all sufficiently large strings.
    • Zimin avoidmers are k-mers that do not contain any Zimin words.

    Purpose of the Study:

    • To investigate the presence and distribution of Zimin avoidmers in the human genome.
    • To analyze the genomic localization and properties of Zimin avoidmers.
    • To compare Zimin avoidmer frequencies and localization across diverse organisms.

    Main Methods:

    • Analysis of k-mer patterns within the human genome reference.
    • Identification and characterization of Zimin avoidmers.
    • Comparative genomics across eight model organisms from three domains of life.

    Main Results:

    • In the human genome, all k-mers >104 bp contain Zimin words.
    • Zimin avoidmers are enriched in coding and Human Satellite 1 regions.
    • Zimin avoidmers exhibit lower germline insertion and deletion rates.
    • Genomic density of Zimin avoidmers varies significantly across species, highest in prokaryotes (E. coli) and lowest in eukaryotes (D. rerio).
    • The longest k-mer length for Zimin avoidmers observed was 115 bp in S. cerevisiae.

    Conclusions:

    • Zimin avoidmers show inhomogeneous genomic distributions and unique properties, including reduced mutation rates.
    • Their prevalence and localization differ substantially across the tree of life.
    • Zimin avoidmers disappear faster than theoretically expected across studied genomes.