I have rna-seq psuedoalignments for a genome with a lot of paralogs. I suspect there are some errors/complications with multi-mapping reads. Focusing on one transcript, I have a multiple sequence alignment of all its paralogs and can easily see their overlaps and homology. Separately, I have a bam file for my transcript and can see where the reads are aligning. I'm trying to get a sense for which of the reads are in a conserved region across the paralogs and which (if any) are in a region unique to the transcript of interest. But to do so I have to keep flipping back and forth between the two and counting positions. Does anyone know of a way to view both in one place? Like is there a way to convert the MSA file (currently a clustal .aln file) to a bam file with one of the sequences as a reference? Or a bunch of pairwise alignments? Or do I need to convert the information I want from the MSA alignment to a bed file and add that? Any suggestions would be greatly appreciated!