Fig. 5

Illustration of MRF’s merit in handling repeat-rich regions, with WSSV case. For BLAST search, query is coding sequences of AF332093 genome and the subject is KX686117 genome. For MRF run, the query is KX686117 genome [300223 bp] and the reference is AF332093 genome [305119 bp]. A Summary of results from BLAST search and MRF run for the CDS, wsv178. In wsv178, there are overlapping repeat regions of 66 bp in AF332093 accession. Every repeat region shares a 12 bp sequence with previous repeat region. The BLAST reported a hit in subject genome with 100% similarity and 100% query coverage however MRF reported deletion of 58.09% of CDS length. B The alignments reported for wsv178 by BLAST. Here, several repeat regions in query genome made multiple alignments across single repeat region of subject genome leading to a positive hit with 100% query coverage. This lead to BLAST failing to report partial deletions in wsv178. As MRF relies on exact matches, it could report partial deletions in repeat regions of wsv178. C Depiction of repeat regions of wsv178 and the alignments made by BLAST between query and subject. D Depiction of repeat regions of wsv178 and the exact matches made by MRF between query and reference genomes