Hello, I'm facing a problem where I'm trying to map all the "events" on the query sequence (the new genome) to the reference genome. The problem is, MIRA inserts several * on the reference prior to assembly and shift frames (as reported in the AT field in the MAF file). After all those modification I'm not able to map BACK base-by-base each problem. I'm planning on creating a "multiple alignment" of the two sequences for high density annotation. Can anyone help me? Regards