Is this behavior a result of strand specificity? For example, on the first line would "FUN_003800-T1" be on the negative strand while "FUN_003804-T1" on the positive strand so the ssend would be a smaller value than the sstart?
Yes, the match is on the negative strand.
Yes the query is aligned with the reversed complement of the target(subject). Blast has an option -strand that can be set to plus, minus, both. If you only want matches from the positive strand you can use -strand plus.
Please see the link below for more information on matching with negative strand:
I just wanted to add for the record that the sstart and send coordinates are all relative to the same reference strand you used for BLAST, regardless of which strand your query sequence aligned to. In other words, for all hits where (send-sstart) < 0, you can simply flip the two coordinates (i.e. assign send to sstart and vice versa) if you need consistency (e.g. when creating a GRanges object which requires send > sstart).
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version 2.3.6
Ok, that's what I thought but I couldn't find it in the documentation and just wanted to be sure. Can you put this as an answer so I can mark it correct?