Nearrepeats

Nearrepeats, also called near repeats, are pairs or clusters of DNA sequences that share high sequence similarity and are located near each other in the genome. Unlike fully identical repeats, near repeats show small sequence differences that have accumulated since their common origin. They are typically identified by local sequence alignments within a defined genomic window, with substantial identity and a close physical separation, ranging from a few hundred bases to several kilobases.

Near repeats arise through duplication events or through processes such as replication slippage, unequal crossing over, or the activity of transposable elements, which generate related sequences in close proximity. Their formation can create blocks of related sequence that diverge slightly over time.

Biological significance of near repeats includes serving as substrates for non-allelic homologous recombination, which can generate structural variation such as deletions, duplications, and inversions. They influence genome organization and evolution and can contribute to the expansion of gene families or to local genome instability in some contexts.

Detection and analysis typically involve identifying pairs of similar sequences within a local genomic neighborhood using sequence comparison tools such as BLAST, MUMmer, or specialized repeat-finding pipelines. Researchers apply thresholds for length and percent identity and define acceptable inter-repeat distances according to the study goals. Annotation is often integrated with broader repeat annotation resources, including segmental duplications and low-copy repeats.

Distribution of near repeats is widespread across taxa, including plants, animals, and microbes. In many genomes, near repeats overlap with other classes of repeats and can complicate assembly and analysis, while also providing insight into mechanisms of duplication and rearrangement. The term is used variably in literature, and definitions may differ in the exact criteria used to classify a sequence as a near repeat.