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The output of DIALIGN is a mapping of the query sequence coordinates to various reference sequence coordinates (i.e. regions).
The coding sequence coordinates of the probes for viral suppressors of silencing were: P38, nucleotides 42 to 472; HC-Pro, entire coding sequence.
The sequence coordinates of B3, ARF and AP2 domains plus E-value showed for B3 domain were annotated according to Pfam databases [67].
We decided against using sequence coordinates to track physical distances because this value was cumbersome and not readily derived from the locus number.
The genome sequence was reformatted so that dnaA was the first gene and sequence coordinates were reassigned before submitting the sequence for gene predictions.
The first step was to re-format the sequence so that dnaA was the first gene and then reassign the sequence coordinates before submitting the sequence for gene predictions.
To simulate an approximately 100 kb region of centromeric DNA, we strung together six copies of the 16,545 bp centromeric DNA sequence (coordinates 563335 578794) from the end of this contig.
cAll sequence coordinates are given in amino acid residues.
All sequence coordinates in this study are from GRCh37/hg19.
Shivaswamy et al. [ 8] directly provided sequence coordinates for the inferred nucleosome positions.
Boundary element sequence coordinates were retrieved from available literature [ 46, 58].
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