Hi community.

I am on a mission of retrieving upstream sequences of my contigs blasted to cotton genome(http://www.phytozome.net/search.php), the alignment was at chr2: 110580 to 110980, then I want upstream. In that process I found something interesting that when I given the coordinates of chr: 108580 to110580 the result was 2001bp but when the same coordinates are changed like chr:110580 to 108580 the result was -1999bp(minus) and the two upstream strands are completely different. suggest me which coordinates will retrieve exact upstream of my contigs.