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A final sorting was performed within each subclass: FRT-like sequences were sorted based on their spacer sequences (in both direct and inverse complement orientations) to identify those FRT-like sequences that have identical spacers and therefore can potentially recombine with each other (Text S7).
Sequences for KSHV, EBV, and a set of control genes (additional file 1, Table S9) were uploaded in FASTA format in forward and reverse complement orientations onto the eArray probe design website (https://earray.chem.agilent.com/earray/) [ 57].
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LCBs below a plasmid's center line represent the reverse complement orientation relative to the reference genome (pCP13, Fig. 7; pCLL, Fig. 8).
The numbers in both the forward and reverse complement orientation of the proximal-8 region are compared, with the lowest value used for the filename designation.
Primer II: TTY1…Y21ACAAAAAGATCAAGGC (Y1-Y21 are the amiR sequence in reverse complement orientation).
Outputs specifically identify Helitron sequences as being in a forward or reverse complement orientation.
An EST was detected (GenBank accession AW777232) whose sequence was an exact match to a portion of the grn1 gene, but in the reverse complement orientation.
An inverted repeat (IR) occurs when two exact or approximate copies of a particular DNA sequence are present in reverse complement orientation.
This observation prompted a search for sequences deposited at GenBank corresponding to parts of the grna cDNA sequence, but in the reverse complement orientation.
In addition, ASgrn1-2 harboursequenceses for an extensively mutated tzf transposon (Tc1/mariner superfamily) in its last exon, but in the reverse complement orientation.
In cases where the primer is found in the reverse complement orientation, it is a good idea to reverse complement the sequence so that all reads are in the same orientation for the remaining analysis steps.
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