Next the BlastN output is parsed to retain only copies matching both ends of the query and extracting the first and last 10 bp of each element plus 50 bp of flanking genomic sequence on each side.
The copy number of "r" repeats varies from 2 to 6: r11, r12, r13, r15, r15 -> two copies matching perfectly expect one difference in r11; r03, r04, r06, r14, r14 -> found three time in the genome (r01 and r14 are presenting polymorphisms); r05 and r07 -> five copies (r05 is the most polymorphic "r" repeat); r08 and r10 - 6 copies (r08 is very conserved).
To select single copy completely matched probes, similarities of all 628,725 PM probe target sequences of the Affymetrix GeneChip® array were searched against the Nipponbare genome by BLASTN analysis (Table 1).
Of the three SeubFLO genes (FLO1, FLO5, and FLO10), only FLO1 did not exhibit a copy number matching the chromosomal copy number in all strain variants, as it was not identified in the A1 strain.
Each of these clades contains the gene copies from matching locations within the Huge Repeat unit.
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If a promoter has multiple matched copies of the input core motif, all copies are extracted and aligned to create an initialization of the PSWM of the target genes.
The process of copying (matching) is exactly defined under the Heredity section.
In order to assemble each gene copy, matching reads for each reference gene were identified from a database of all trimmed reads from each endophyte genome, through a similarity search using BLAST, defining the E value threshold as 0.1.
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