Hello, currently, I am working on the chloroplast genome and experiencing difficulties in reading ambiguous code N in the intron. I have blasted it to NCBI, but there are no nucleotides aligned with my sample. Furthermore, I have also read the trimmed bowtie2 results, but no nucleotides are matching the reference (references were missing nucleotides). Is there any advice on what I can do to obtain the actual reading of the ambiguous code N? Thank you