Table 4.

CRISPR-Cas systems identified in the studied strains by CRISPR-finder

Strain	Predicted CRISPR	Start	End	Size	DR (nt)	No. spacers	Type	Immunity to identified phages	Immunity to mobile elements identified in this study	Locus ID	Note
JS	Crispr_2	2,424,099	2,427,021	2922	36	40	IU	Anatole, B3, B22, E1, E6, G4, PFR1, PFR2	PJS22, PJS23, PJS7, pJS12	PFREUDJS001_002141-PFREUDJS001_002147	–
JS2	Crispr_3	2,082,550	2,088,376	5826	28	95	IE	B22, B3, E1,E6, G4, Anatole, Doucette, PFR1, PFR2	PJS22, PJS23, PJS7, pJS25	PFR_JS2_1825-PFR_JS2_1832	–
	Crispr_4	2,120,759	2,122,610	1851	36	25	IU	PFR1, PFR2	PJS7	PFR_JS2_1843-PFR_JS2_1849	–
JS4	Crispr_3	1,825,170	1,827,746	2576	36	35	IU	Doucette, E6, G4, PFR1, PFR2	PJS22, PJS7, pJS25	PFR_JS4_1650-PFR_JS4_1655	One system, negative strand, spacers separated by a transposase gene and then by a four-gene integron.
	Crispr_2	1,823,162	1,823,697	535	36	7		–	–
	Crispr_1	1,818,598	1,819,215	617	36	8		–	–
JS7	Crispr_2	2,203,337	2,207,335	3998	28	65	IE	B22, B3, E1,E6, G4, Anatole, Doucette, PFR1, PFR2	PJS22, PJS7, pJS12	PFR_JS7–1_1964-PFR_JS7–1_1971	No cas2
JS8	Crispr_3	2,192,257	2,196,491	4234	36	58	IU	Anatole, Doucette, B3, B22, E1, E6, G4, PFR1, PFR2, phiB5	PJS22, PJS23, PJS7, pJS25	PFR_JS8_1930-PFR_JS8_1935	–
JS9	Crispr_3	2,260,079	2,260,655	576	28	9	IE	–	–	PFR_JS9–1_2018-PFR_JS9–1_2025	One system, negative strand, spacers separated by an integrase
	Crispr_2	2,253,046	2,258,937	5891	28	96		B22, B3, E1,E6, G4, Anatole, Doucette, PFR1, PFR2, phiB5	–
	Crispr_4	2,288,755	2,292,746	3991	29	65	N/A	Doucette, B3, B22, G4, PFR1, PFR2	PJS23, PJS7		Remnant of a system, no Cas. Spacers separated by an integrase.
	Crispr_5	2,293,887	2,295,016	1129	29	18		PFR1, PFR2	PJS7
JS10	Crispr_2	2,029,533	2,032,236	2703	36	37	IU	Anatole, B3, B22, E1, E6, G4, PFR1, PFR2	PJS22, PJS23, PJS7, pJS12	PFR_JS10_1797-PFR_JS10_1803
JS12	Crispr_1	2,181,462	2,185,411	3949	36	54	IU	Doucette, B3, B22, E6, G4, PFR1, PFR2, phiB5	PJS22, PJS23, PJS7	PFR_JS12–1_1906-PFR_JS12–1_1911
JS14	PossibleCrispr_1	1,595,184	1,595,290	106	36	1	N/A	Anatole, E1		PFR_JS14_1397
JS15_1	Crispr_1	441,841	444,266	2425	36	33	IU	Anatole, B3, B22, E1, E6, G4, phiB5	PJS23, pJS12	PFR_JS15–1_371-PFR_JS15–1_376
JS16	Crispr_2	417,820	419,522	1702	36	23	IU	B22, E6, G4, PFR1, PFR2	PJS22, PJS23, PJS7	RM25_0342-RM25_0347	One system, negative strand, spacers separated by a transposase gene. Both CRISPR stretches carry immunity to known phages.
	Crispr_1	413,342	416,347	3005	36	41		Anatole, B3, B22, E1, E6	PJS22
JS17_1	Crispr_2	2,220,735	2,225,402	4667	36	64	IU	Anatole, Doucette, B3, B22, E1, PFR1, PFR2	PJS22, PJS23, pJS12, pJS25	PFR_JS17–1_1953-PFR_JS17–1_1958	–
JS20_1	Crispr_3	2,034,463	2,037,183	2720	36	37	IU	Doucette, B22, E6, G4, PFR1, PFR2	PJS23, PJS7	PFR_JS20–1_1815-PFR_JS20–1_1820	One system, spacers separated by a transposase gene and then by an eight-gene integron.
	Crispr_4	2,038,656	2,039,048	392	36	5		–	–
	Crispr_5	2,044,247	2,044,936	689	36	9		–	–
JS21_1	Crispr_5	2,189,758	2,192,624	2866	36	39	IU	Doucette, E6, G4, PFR1, PFR2	PJS22, PJS7, pJS25	PFR_JS21–1_1963-PFR_JS21–1_1968	One system, negative strand, the spacers separated by a transposase gene and then by a four-gene integron.
	Crispr_4	2,187,750	2,188,285	535	36	7		–	–
	Crispr_3	2,183,185	2,183,803	618	36	8		–	–
JS22	Crispr_2	2,150,779	2,151,318	539	36	7	IU	–	–		Remnant of the same IU system, but no Cas. No immunity to known phages found.
JS23	Crispr_2	2,124,520	2,126,512	1992	36	27	IU	Anatole, B3, B22, E1, E6, G4, phiB5	PJS23	PFR_JS23_1889-PFR_JS23_1894	–
JS25	Crispr_2	2,042,081	2,045,018	2937	36	40	IU	Doucette, E6, PFR1, PFR2	PJS22,PJS7,pJS25	PFR_JS25–1_1807-PFR_JS25–1_1812	One system, spacers separated by a transposase gene and then by a four-gene integron.
	Crispr_3	2,046,491	2,046,954	463	36	6		–	–
	Crispr_4	2,050,901	2,051,519	618	36	8		–	–