In a illumina paired end sequencing output file, are both the two corresponding sequences in the same orientation (like both are in 5' to 3') or are they in different orientaions (like one in 5' to 3' and other one in 3' to 5')?
Sequence reads are always in 5'-->3' orientation. See: Orientation in paired-end sequencing? . Mappers will automatically reverse complement reads (as needed) when mapping the reads.