File looks like this:
99_999_852_F3	chr9	97768833	97768867	ATTTTCTTCAATTACATTTCCAATGCTATCCCAAA	+	35
99_999_852_F3	chr9	97885645	97885679	ATTTTCTTCAaTTACATTTCCAATGCTATCCCAAA	+	35
99_99_994_F3	chr10	47028821	47028855	AGACAAAAAGGCCATCAACAGATCAGTAAAGGATC	+	35
...