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`? 

![enter image description here][1]


  [1]: https://i.imgur.com/Gn5Aukn.png
Yes, the match is on the negative strand.