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While the exact causes of excessive variability in a specific repeat tract remain an open question, several features are generally agreed to contribute to high variability of repetitive sequences: length (i.e., number of repeats), purity (i.e., number of interruptions to the repetitive pattern) and sequence (i.e., the nucleotide sequence being repeated) [ 7, 8].
Therefore, if the user is interested in a specific repeat and it has not been reported, possibly as a result of the emergence of indels in the flanking sequences, we recommend decreasing the flank length and/or also increasing the mismatch tolerance.
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For example, "AG@Coding" in Ensembl gene id "ENSG00000069329" represents a specific repeated pattern "AG" appearing within the coding region of "ENSG00000069329".
The classical dogma states that cleavage only occurs when the two sites are in a specific inverted repeat, such that the sites are 'head-to-head' [ 3, 11, 12].
We noticed that even for the H3K9me3 and H3K9me2 heterochromatic marks that are enriched in short repeats a few specific repeat sequences are depleted of these marks.
We next examined the substitution rate correlation in specific repeat classes and subclasses.
This paper is intended to assist the experts during the creativity phase of value engineering through utilizing the past experiences and avoid them in a specific domain from repeating the same experience.
We have demonstrated that transposon Tn7 will recognize structures that form spontaneously in GAATTC repeats and insert in a specific orientation within the repeat.
In addition to the already masked region identified by RepeatMasker, we also ignored variants in specific repeats in the EBV genome reference genome (NC_007605) according to GenBank annotation.
To help in banana sequence annotation, a specific Musa repeat database was created, and its utility was demonstrated by analyzing the repeat composition of 62 genomic BAC clones.
In contrast, the beneficial effects on host fitness may vary in different environments, and in some microorganisms specific repeats may just be parasitic DNA.
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