assembly_id	genome_id	genome_def	crispr_array_locus_merge	crispr_array_location_merge	crispr_locus_id	crispr_pred_method	array_in_prot	prot_within_array_20000	prot_in_genome	crispr_type_by_cas_prot	consensus_repeat	repeat_length	self-targeting_spacer_number	self-targeting_target_number	spacer_location	protospacer_location	repeat_type	spacer_locus_num	spacer_num	correct_crispr_type	genome_cas_prots	unknown_protein_around_crispr	L10	L10_domain	L9	L9_domain	L8	L8_domain	L7	L7_domain	L6	L6_domain	L5	L5_domain	L4	L4_domain	L3	L3_domain	L2	L2_domain	L1	L1_domain	R1	R1_domain	R2	R2_domain	R3	R3_domain	R4	R4_domain	R5	R5_domain	R6	R6_domain	R7	R7_domain	R8	R8_domain	R9	R9_domain	R10	R10_domain
GCF_002209225.1_ASM220922v2	NZ_CP022070	Salmonella enterica subsp. enterica serovar Typhimurium strain FDAARGOS_321 chromosome, complete genome	1	2265487-2266857	1,1,1	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	DEDDh,RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	21,22,22	22	TypeI-E	DEDDh,RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DinG	NA,NA	NA|381aa|up_9|NZ_CP022070.1_2251285_2252428_+	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism]	NA|919aa|up_8|NZ_CP022070.1_2252471_2255228_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|432aa|up_7|NZ_CP022070.1_2255285_2256581_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_6|NZ_CP022070.1_2256632_2258867_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|119aa|up_5|NZ_CP022070.1_2258950_2259307_+	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]	NA|99aa|up_4|NZ_CP022070.1_2259272_2259569_+	COG3668, ParE, Plasmid stabilization system protein [General function prediction only]	NA|267aa|up_3|NZ_CP022070.1_2260336_2261137_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|NZ_CP022070.1_2261364_2263002_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|NZ_CP022070.1_2263084_2264383_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|NZ_CP022070.1_2264518_2265190_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|NZ_CP022070.1_2266954_2267752_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|NZ_CP022070.1_2267839_2268202_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|600aa|down_2|NZ_CP022070.1_2268625_2270425_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_3|NZ_CP022070.1_2270424_2272137_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_4|NZ_CP022070.1_2272212_2272947_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_5|NZ_CP022070.1_2273034_2273988_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|down_6|NZ_CP022070.1_2274432_2277096_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|down_7|NZ_CP022070.1_2277107_2278664_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|down_8|NZ_CP022070.1_2278660_2279221_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|down_9|NZ_CP022070.1_2279234_2280293_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI
GCF_002209225.1_ASM220922v2	NZ_CP022070	Salmonella enterica subsp. enterica serovar Typhimurium strain FDAARGOS_321 chromosome, complete genome	2	2282989-2283508	2,2,2	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	DEDDh,RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACC,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	28,29,29	0	0	NA	NA	I-E:I-E:I-E	7,8,8	8	TypeI-E	DEDDh,RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DinG	NA,NA	NA|245aa|up_9|NZ_CP022070.1_2272212_2272947_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP022070.1_2273034_2273988_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP022070.1_2274432_2277096_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP022070.1_2277107_2278664_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP022070.1_2278660_2279221_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP022070.1_2279234_2280293_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP022070.1_2280303_2281050_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP022070.1_2281031_2281682_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP022070.1_2281678_2282599_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP022070.1_2282598_2282892_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP022070.1_2284173_2285220_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP022070.1_2285470_2286379_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP022070.1_2286388_2287828_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP022070.1_2287814_2288420_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP022070.1_2288470_2288794_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP022070.1_2288984_2289296_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP022070.1_2289314_2290025_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP022070.1_2290024_2290504_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP022070.1_2290500_2291550_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP022070.1_2291530_2292292_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_002209225.1_ASM220922v2	NZ_CP022070	Salmonella enterica subsp. enterica serovar Typhimurium strain FDAARGOS_321 chromosome, complete genome	3	2283582-2284159	3,3,3	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	DEDDh,RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	8,9,9	9	TypeI-E	DEDDh,RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DinG	NA,NA	NA|245aa|up_9|NZ_CP022070.1_2272212_2272947_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP022070.1_2273034_2273988_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP022070.1_2274432_2277096_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP022070.1_2277107_2278664_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP022070.1_2278660_2279221_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP022070.1_2279234_2280293_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP022070.1_2280303_2281050_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP022070.1_2281031_2281682_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP022070.1_2281678_2282599_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP022070.1_2282598_2282892_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP022070.1_2284173_2285220_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP022070.1_2285470_2286379_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP022070.1_2286388_2287828_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP022070.1_2287814_2288420_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP022070.1_2288470_2288794_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP022070.1_2288984_2289296_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP022070.1_2289314_2290025_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP022070.1_2290024_2290504_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP022070.1_2290500_2291550_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP022070.1_2291530_2292292_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_002209225.1_ASM220922v2	NZ_CP022070	Salmonella enterica subsp. enterica serovar Typhimurium strain FDAARGOS_321 chromosome, complete genome	4	2475086-2475195	4	CRISPRCasFinder	no		DEDDh,RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DinG	Orphan	TGTCCCACCCTGTACCACTTTTTTTTAA	28	0	0	NA	NA	NA	1	1	Orphan	DEDDh,RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DinG	NA,NA|276aa|down_2|NZ_CP022070.1_2477983_2478811_+,NA|198aa|down_4|NZ_CP022070.1_2480728_2481322_-,NA|76aa|down_7|NZ_CP022070.1_2485770_2485998_-	NA|212aa|up_9|NZ_CP022070.1_2466461_2467097_+	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase	NA|401aa|up_8|NZ_CP022070.1_2467170_2468373_-	pfam13020, DUF3883, Domain of unknown function (DUF3883)	NA|338aa|up_7|NZ_CP022070.1_2468667_2469681_-	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|327aa|up_6|NZ_CP022070.1_2469691_2470672_-	COG3732, SrlE, Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism]	NA|125aa|up_5|NZ_CP022070.1_2470668_2471043_-	COG3731, SrlB, Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]	NA|174aa|up_4|NZ_CP022070.1_2471039_2471561_-	COG3730, SrlA, Phosphotransferase system sorbitol-specific component IIC [Carbohydrate transport and metabolism]	NA|95aa|up_3|NZ_CP022070.1_2471673_2471958_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|119aa|up_2|NZ_CP022070.1_2472052_2472409_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|273aa|up_1|NZ_CP022070.1_2472563_2473382_-	pfam14491, DUF4435, Protein of unknown function (DUF4435)	NA|428aa|up_0|NZ_CP022070.1_2473426_2474710_-	COG3950, COG3950, Predicted ATP-binding protein involved in virulence [General function prediction only]	NA|690aa|down_0|NZ_CP022070.1_2475212_2477282_-	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|72aa|down_1|NZ_CP022070.1_2477317_2477533_-	COG3311, AlpA, Predicted transcriptional regulator [Transcription]	NA|276aa|down_2|NZ_CP022070.1_2477983_2478811_+	NA	NA|398aa|down_3|NZ_CP022070.1_2479145_2480339_-	pfam02810, SEC-C, SEC-C motif	NA|198aa|down_4|NZ_CP022070.1_2480728_2481322_-	NA	NA|778aa|down_5|NZ_CP022070.1_2483105_2485439_-	COG3378, COG3378, Phage associated DNA primase [General function prediction only]	NA|107aa|down_6|NZ_CP022070.1_2485453_2485774_-	pfam17345, DUF5375, Family of unknown function (DUF5375)	NA|76aa|down_7|NZ_CP022070.1_2485770_2485998_-	NA	NA|184aa|down_8|NZ_CP022070.1_2485994_2486546_-	pfam10554, Phage_ASH, Ash protein family	NA|89aa|down_9|NZ_CP022070.1_2486542_2486809_-	COG3311, AlpA, Predicted transcriptional regulator [Transcription]
GCF_002209225.1_ASM220922v2	NZ_CP022072	Salmonella enterica subsp. enterica serovar Typhimurium strain FDAARGOS_321 plasmid unnamed2, complete sequence	1	18607-18726	1	CRISPRCasFinder	no			Orphan	TGCGTACCCATCCACCTTTCAGTGCGTACCCATCCACCTTTCA	43	0	0	NA	NA	NA	1	1	Orphan	DEDDh,RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DinG	NA|258aa|up_9|NZ_CP022072.1_11031_11805_-,NA|150aa|up_8|NZ_CP022072.1_11949_12399_+,NA|28aa|up_7|NZ_CP022072.1_13146_13230_+,NA|95aa|up_4|NZ_CP022072.1_15171_15456_+,NA|142aa|up_2|NZ_CP022072.1_16538_16964_-,NA|149aa|up_1|NZ_CP022072.1_17031_17478_-,NA|108aa|down_2|NZ_CP022072.1_20252_20576_+,NA|82aa|down_3|NZ_CP022072.1_20620_20866_+,NA|72aa|down_4|NZ_CP022072.1_20855_21071_+,NA|110aa|down_5|NZ_CP022072.1_21163_21493_+,NA|60aa|down_6|NZ_CP022072.1_21535_21715_+,NA|50aa|down_7|NZ_CP022072.1_21784_21934_+,NA|91aa|down_8|NZ_CP022072.1_21946_22219_+,NA|182aa|down_9|NZ_CP022072.1_22544_23090_+	NA|258aa|up_9|NZ_CP022072.1_11031_11805_-	NA	NA|150aa|up_8|NZ_CP022072.1_11949_12399_+	NA	NA|28aa|up_7|NZ_CP022072.1_13146_13230_+	NA	NA|215aa|up_6|NZ_CP022072.1_13384_14029_-	cd03767, SR_Res_par, Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme	NA|221aa|up_5|NZ_CP022072.1_14409_15072_+	PHA02518, PHA02518, ParA-like protein; Provisional	NA|95aa|up_4|NZ_CP022072.1_15171_15456_+	NA	NA|78aa|up_3|NZ_CP022072.1_16253_16487_+	pfam14317, YcxB, YcxB-like protein	NA|142aa|up_2|NZ_CP022072.1_16538_16964_-	NA	NA|149aa|up_1|NZ_CP022072.1_17031_17478_-	NA	NA|279aa|up_0|NZ_CP022072.1_17517_18354_-	pfam01051, Rep_3, Initiator Replication protein	NA|84aa|down_0|NZ_CP022072.1_19584_19836_+	PRK02854, PRK02854, primosomal protein DnaT	NA|94aa|down_1|NZ_CP022072.1_19825_20107_+	COG2026, RelE, Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]	NA|108aa|down_2|NZ_CP022072.1_20252_20576_+	NA	NA|82aa|down_3|NZ_CP022072.1_20620_20866_+	NA	NA|72aa|down_4|NZ_CP022072.1_20855_21071_+	NA	NA|110aa|down_5|NZ_CP022072.1_21163_21493_+	NA	NA|60aa|down_6|NZ_CP022072.1_21535_21715_+	NA	NA|50aa|down_7|NZ_CP022072.1_21784_21934_+	NA	NA|91aa|down_8|NZ_CP022072.1_21946_22219_+	NA	NA|182aa|down_9|NZ_CP022072.1_22544_23090_+	NA
