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Repeats (30-500 bp) were discovered using in-house private commercial software developed by Shanghai Majorbio Bio-pharm Biotechnology Company (China).
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Short repeat sequences including direct and inverted repeats in pt genome were discovered using REPuter [ 84] at repeat length of at least 30 bp and with a Hamming distance of 3. Tandem repeats were detected by Tandem Repeat Finder V4.0.4.
(4) De novo motif analysis on the central 100-bp peak regions was carried out using the Homer software (Heinz et al, 2010), and matches to known motifs were discovered using TOMTOM (Gupta et al, 2007).
These motifs were discovered using MERCI software.
SNPs were discovered using Varscan [ 49].
SNPs were discovered using two different strategies.
Differentially methylated regions were discovered using a Fisher Exact Test, with a p-value threshold of 0.05, a minimum of 3 DMCs in a region, and a maximum distance of 300 bp between DMCs.
Both SNPs and small indels (<2 bp) were discovered and were confirmed by capillary sequencing.
Six additional non-coding regions larger than 30 bp were discovered.
The association of rs1051317 at 142,626,120 bp was discovered in individuals of Korean ancestry [25].
Peptidic linkers specific for 6 bp sequences of double-stranded DNA were discovered by using DNase I footprinting to screen NDI bisintercalator libraries.
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