I've done Blast alignment for one protein against the whole genome. The results are confusing because there are identical alignments with different results.
One of the examples:
I've used Biolinux and Blast+ 2.6.1
Do you have any ideas why that have happened?
BLAST is a local alignment method - it can and will give multiple alignments between a single query and target pair, depending on how run. From quick look - I'd guess those are two different sub-sequences of your query (SCO2792) aligning to different sub-sequences of the target (SCO0697), with high alignment scores. The 2 local alignments you show between the query and target have different start and end coordinates, lengths, expectation scores, etc. that are shown in your table. Use the column headers you list above in the comments to read off the start and end coordinates of each of the two alignments in the query and target.