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Boxwell: A ritual is any interaction that is repeated, coordinated, and emotionally resonant.
The crystal structures were refined by removing water molecules and repeating coordinates.
For each chromosome, gene coordinates and repeat coordinates and details were recorded.
CpG islands and simple nucleotide repeat coordinates were obtained from the UCSC Genome Browser [ 72].
Repeat coordinates were identified using the slow option of RepeatMasker v3.0.5 with an updated RepBase library for cattle.
SNPs in repeat regions were removed (repeat coordinates in mm4 were downloaded from UCSC annotation server), which left a total of 484,727 Celera and 24,332 dbSNPs.
The complete set of results was tabulated strain wise, with features such as the repeat coordinates, copy number and repeat motif.
Left flanking and right flanking sequences (≤250 bp) of each repeat coordinates were extracted by using a perl program called XTRACT.
Alu and non Alu repeats with HNF4α sites were identified by comparing the HNF4α genome-wide search results to the repeat coordinates obtained from Repeat Masker Track version 3.2.7 in UCSC Genome Browser.
This file was used as input to a Perl script that used the Ensembl Perl API [ 60] version 15_33 to extract all known genes (Ensembl-predicted transcripts that map to species-specific SwissProt, RefSeq or TrEMBL database entries) whose chromosomal coordinates overlapped with the repeat coordinates.
Indeed, at a Serie A match between Milan and Juventus at San Siro last month, a large group of away fans made repeated and coordinated monkey noises every time one of Milan's black players committed a foul.
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