Maybe a basic question.
I am trying to get the homolog aligned sequences for a huge gene in drosophila (Sls). It spans 75kb, located chr3L:2039681-2115611. I tried to get a MAF file from UCSC table browser, and sent it to galaxy. Then I used the "Join MAF blocks by Species" command to merge the MAf blocks into 27 species. Finally I converted the MAF file to fasta (MAF to Fast command). Everything worked ok except the final fasta alignment file spans a 16kb region instead of 75kb. At some point during the process some regions are being deleted and I don't understand why.