The segmental duplications in the UCSC track show orientation. I wonder how the orientation of these sequences is determined?
Take these two examples. The UCSC seg Dup annotates both of them on minus strands. But when you look at the sequence 5'->3', chrX:155006107-155007147 is in minus-strand, but the other homologous region (chrX:155147781-155148821) is the reverse complement of the chrX:155006107-155007147. The orientation should be in the reverse direction.
I would really appreciate any thought.