Table 1.

Top 10 gRNAs Located in the Core and Enhancer Regions of the LTR U3 Region

Name	Spacer (5′ to 3′)	PVC	Strand	Start	Stop	PCS	Diversity	POC	Functional Motif
LTRgRNA490	CUGCUUUUAUGCAGCAUCUGNGG	0.926	−	416	435	418	1.23	0	TATA box
LTRgRNA49	UGCUUAUAUGCAGCAUCUGANGG	0.922	−	415	434	417	1.31	0	TATA box
LTRgRNA28	CUUUCCGCUGGGGACUUUCCNGG	0.911	+	354	373	370	2.40	1a	NF-κB I
LTRgRNA219	UUUCCGCUGGGGACUUUCCGNGG	0.887	+	355	374	371	2.60	0	NF-κB I
LTRgRNA253	CUUUCCACUGGGGACUUUCCNGG	0.880	+	354	373	370	2.40	3	NF-κB I
LTRgRNA491	UGCUUUUAUGCAGCAUCUGANGG	0.874	−	415	434	417	1.31	1	TATA box
LTRgRNA57	UUUCCGCUGGGGACUUUCCANGG	0.864	+	355	374	371	2.60	0	NF-κB I
LTRgRNA25	CUGCUUAUAUGCAGCAUCUGNGG	0.858	−	416	435	418	1.23	1	TATA box
LTRgRNA24	CUACAAGGGACUUUCCGCUGNGG	0.858	+	344	363	360	2.67	1b	NF-κB II
LTRgRNA65	AUCUACAAGGGACUUUCCGCNGG	0.854	+	342	361	358	2.91	0	NF-κB II

The list was ranked by percent variant coverage (PVC) and predicted off-target counts (POCs). The closest functional motif from a given gRNA was counted by the distance between the predicted cleavage sites (PCSs) and the motif positions on the HIV-1 LTR based on the coordinates of HXB2.

^aLTRgRNA28 (gNFKB0), POC: chr2: 29124850–29124872 (29124856), WDR43 intron 1/17

^bLTRgRNA24 (gNFKB1), POC: chr13: 30403040–30403062 (30403046), UBL3 intron 1/4