Table 1. Details of spacer sequences selected from chilli leaf curl virus (ChiLCV) genome and their final selection based on off-target analysis and GC%.

Genomic region	Nucleotide coordinate and spanning length	Spacer name	Seq	PAM	Off Target analysis (10 top hit)				GC%
					Position in the genome	Target match in NB genome	Seed seq match	PAM match
IR region with origin of replication	1–145 nt, span: 145 nt and 2611–2762, span: 152 nt	IR-Spacer1	CAATCGGTACTCAACAAACT	TGG	2622–2641	no	9–20 match	No	40
		IR-Spacer2	AACAAACTTGGCTATGTAAT	CGG	2634–2653	no	11–21 match	No	30
		IR-Spacer3	*GCCATCCGCACTAATATTAC	CGG	2745–2762, 1–2	no	9–20 match	No	45
		IR-Spacer4	TGGCCGCGATTTTTTTACCG	TGG	7–26 nt	no	12–23 match	Yes	50
		IR-Spacer5	CTCATAGCTTAATTATTTCA	TGG	81–100	no	12–23 match	No	25
		IR-Spacer6	*CATGGTCCCCCCTATAAACT	TGG	99–118	no	12–21 match	No	50
Overlapping betwwen V2 and V1 ORFs (V2/V1)	306 nt– 502 nt, span: 197 nt	V2/V1-Spacer1	*CATTTCCACGCCCGCCTCGA	AGG	332–351	no	12–20 match	No	65
		V2/V1-Spacer2	CCCCACTGTCCGCGTCACAA	AGG	404–423	no	14–23 match	Yes	65
		V2/V1-Spacer3	*AGGCCAGAGCATGGGTGAAC	AGG	424–443	no	12–21 match	No	60
		V2/V1-Spacer4	ACAGGAAGCCCAGGATGTAC	AGG	454–473	no	10–20 match	No	55
Overlapping between C1 and C4 ORFs (C1/C4)	2160–2459 nt, span: 300 nt	C1/C4-Spacer1	*GGACCCTGAATTGATTGCCT	CGG	2185–2204	no	10–21 match	No	50
		C1/C4-Spacer2	*TAGCTGATCTTCCATCGACT	TGG	2241–2260	no	10–20 match	No	45
		C1/C4-Spacer3	CTTTTAGCTCCCTGAATGTT	CGG	2324–2343	no	9–20 match	No	40
		C1/C4-Spacer4	GGTCGAAGAATCTGTTGTTT	TGG	2379–2398	no	11–23 match	Yes	40
		C1/C4-Spacer5	ATTTACCTTCGAATTGTATG	AGG	2409–2428	no	12–23 match	Yes	30
		C1/C4-Spacer6	TGTATGAGGACGTGGAGATG	AGG	2423–2442	no	13–23 match	Yes	50

*Spacer sequences finally selected