I have several BAC sequences each of which contains 2-7 contigs. I need to align these BACs to a pseudomolecule and scaffolds. Basically, I need to identify a region were BAC maps on the pseudomolecule. At the end I need to get statistics such as alignment identity, aln lenth, coverage, start end. I can get all of these information from BLAST megablast. However, since megablast is local, it results in many HSP's obviously. Do you guys have an idea how can I calculate this and find the region on a pseudomolecule where each of my BAC aligns? if yes, then how? I can use bwa as an alternative, however, I dont know how to extract information from .bam file..