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Fig. 11 | BMC Bioinformatics

Fig. 11

From: Magic-BLAST, an accurate RNA-seq aligner for long and short reads

Fig. 11

The first two BLASTN alignments of U00001 on human chromosome 17. U00001 is the query and is shown on the top of each row. The first exon really ends at base 85 of the mRNA, but BLASTN aligns the mRNA query to the first exon as well as an extra base in the intron. The second alignment starts three bases before the beginning of the second exon. BLASTN is not splice aware and aligns beyond the splice site and is not aware of paired end sequencing

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