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_001623765.2_ASM162376v2	NZ_CP014971	Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073 chromosome, complete genome	1	637826-637926	1	CRISPRCasFinder	no		RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	Orphan	GCTTCAGTGGCGAACGTCGTGAA	23	0	0	NA	NA	NA	1	1	Orphan	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	NA,NA|177aa|down_1|NZ_CP014971.2_639444_639975_-	NA|448aa|up_9|NZ_CP014971.2_623904_625248_-	PRK05370, PRK05370, argininosuccinate synthase; Validated	NA|151aa|up_8|NZ_CP014971.2_625875_626328_+	PRK00092, PRK00092, ribosome maturation protein RimP; Reviewed	NA|501aa|up_7|NZ_CP014971.2_626355_627858_+	PRK09202, nusA, transcription elongation factor NusA; Validated	NA|893aa|up_6|NZ_CP014971.2_627882_630561_+	PRK05306, infB, translation initiation factor IF-2; Validated	NA|134aa|up_5|NZ_CP014971.2_630781_631183_+	PRK00521, rbfA, 30S ribosome-binding factor RbfA	NA|315aa|up_4|NZ_CP014971.2_631182_632127_+	PRK05033, truB, tRNA pseudouridine synthase B; Provisional	NA|90aa|up_3|NZ_CP014971.2_632277_632547_+	PRK05626, rpsO, 30S ribosomal protein S15; Reviewed	NA|712aa|up_2|NZ_CP014971.2_632788_634924_+	PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional	NA|295aa|up_1|NZ_CP014971.2_635033_635918_+	PRK11189, PRK11189, lipoprotein NlpI; Provisional	NA|27aa|up_0|NZ_CP014971.2_636023_636104_+	NF033440, small_YrbN, protein YrbN	NA|415aa|down_0|NZ_CP014971.2_638139_639384_+	PRK10483, PRK10483, tryptophan permease; Provisional	NA|177aa|down_1|NZ_CP014971.2_639444_639975_-	NA	NA|240aa|down_2|NZ_CP014971.2_640133_640853_+	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown]	NA|336aa|down_3|NZ_CP014971.2_640830_641838_-	PRK10508, PRK10508, luciferase-like monooxygenase	NA|299aa|down_4|NZ_CP014971.2_642015_642912_-	PRK15447, PRK15447, putative protease; Provisional	NA|332aa|down_5|NZ_CP014971.2_642902_643898_-	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|175aa|down_6|NZ_CP014971.2_644114_644639_+	COG3154, COG3154, Putative lipid carrier protein [Lipid metabolism]	NA|168aa|down_7|NZ_CP014971.2_644632_645136_+	COG3153, COG3153, Predicted acetyltransferase [General function prediction only]	NA|106aa|down_8|NZ_CP014971.2_645122_645440_-	PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated	NA|148aa|down_9|NZ_CP014971.2_645477_645921_+	PRK03467, PRK03467, hypothetical protein; Provisional
GCF_001623765.2_ASM162376v2	NZ_CP014971	Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073 chromosome, complete genome	2	987888-989869	1,2,1	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	31,32,32	32	TypeI-E	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	NA,NA	NA|381aa|up_9|NZ_CP014971.2_973686_974829_+	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism]	NA|919aa|up_8|NZ_CP014971.2_974872_977629_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|432aa|up_7|NZ_CP014971.2_977686_978982_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_6|NZ_CP014971.2_979033_981268_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|119aa|up_5|NZ_CP014971.2_981351_981708_+	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]	NA|99aa|up_4|NZ_CP014971.2_981673_981970_+	COG3668, ParE, Plasmid stabilization system protein [General function prediction only]	NA|267aa|up_3|NZ_CP014971.2_982737_983538_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|NZ_CP014971.2_983765_985403_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|NZ_CP014971.2_985485_986784_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|NZ_CP014971.2_986919_987591_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|NZ_CP014971.2_989966_990764_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|NZ_CP014971.2_990851_991214_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|600aa|down_2|NZ_CP014971.2_991637_993437_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_3|NZ_CP014971.2_993436_995149_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_4|NZ_CP014971.2_995224_995959_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_5|NZ_CP014971.2_996046_997000_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|down_6|NZ_CP014971.2_997444_1000108_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|down_7|NZ_CP014971.2_1000119_1001676_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|down_8|NZ_CP014971.2_1001672_1002233_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|down_9|NZ_CP014971.2_1002246_1003305_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI
GCF_001623765.2_ASM162376v2	NZ_CP014971	Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073 chromosome, complete genome	3	1006001-1007014	2,3,2	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	15,16,16	16	TypeI-E	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	NA,NA	NA|245aa|up_9|NZ_CP014971.2_995224_995959_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP014971.2_996046_997000_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP014971.2_997444_1000108_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP014971.2_1000119_1001676_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP014971.2_1001672_1002233_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP014971.2_1002246_1003305_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP014971.2_1003315_1004062_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP014971.2_1004043_1004694_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP014971.2_1004690_1005611_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP014971.2_1005610_1005904_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP014971.2_1007496_1008543_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP014971.2_1008793_1009702_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP014971.2_1009711_1011151_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP014971.2_1011137_1011743_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP014971.2_1011793_1012117_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP014971.2_1012307_1012619_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP014971.2_1012637_1013348_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP014971.2_1013347_1013827_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP014971.2_1013823_1014873_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP014971.2_1014853_1015615_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_001623765.2_ASM162376v2	NZ_CP014971	Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073 chromosome, complete genome	4	1007088-1007482	3,4,3	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACC,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	28,29,29	0	0	NA	NA	I-E:I-E:I-E	6,6,6	6	TypeI-E	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	NA,NA	NA|245aa|up_9|NZ_CP014971.2_995224_995959_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP014971.2_996046_997000_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP014971.2_997444_1000108_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP014971.2_1000119_1001676_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP014971.2_1001672_1002233_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP014971.2_1002246_1003305_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP014971.2_1003315_1004062_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP014971.2_1004043_1004694_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP014971.2_1004690_1005611_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP014971.2_1005610_1005904_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP014971.2_1007496_1008543_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP014971.2_1008793_1009702_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP014971.2_1009711_1011151_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP014971.2_1011137_1011743_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP014971.2_1011793_1012117_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP014971.2_1012307_1012619_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP014971.2_1012637_1013348_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP014971.2_1013347_1013827_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP014971.2_1013823_1014873_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP014971.2_1014853_1015615_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_001623765.2_ASM162376v2	NZ_CP014971	Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073 chromosome, complete genome	5	1198399-1198508	5	CRISPRCasFinder	no		RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	Orphan	TGTCCCACCCTGTACCACTTTTTTTTAA	28	0	0	NA	NA	NA	1	1	Orphan	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	NA,NA|276aa|down_2|NZ_CP014971.2_1201296_1202124_+,NA|198aa|down_4|NZ_CP014971.2_1204041_1204635_-	NA|212aa|up_9|NZ_CP014971.2_1189775_1190411_+	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase	NA|401aa|up_8|NZ_CP014971.2_1190484_1191687_-	pfam13020, DUF3883, Domain of unknown function (DUF3883)	NA|338aa|up_7|NZ_CP014971.2_1191981_1192995_-	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|327aa|up_6|NZ_CP014971.2_1193005_1193986_-	COG3732, SrlE, Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism]	NA|125aa|up_5|NZ_CP014971.2_1193982_1194357_-	COG3731, SrlB, Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]	NA|174aa|up_4|NZ_CP014971.2_1194353_1194875_-	COG3730, SrlA, Phosphotransferase system sorbitol-specific component IIC [Carbohydrate transport and metabolism]	NA|95aa|up_3|NZ_CP014971.2_1194987_1195272_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|119aa|up_2|NZ_CP014971.2_1195366_1195723_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|273aa|up_1|NZ_CP014971.2_1195876_1196695_-	pfam14491, DUF4435, Protein of unknown function (DUF4435)	NA|428aa|up_0|NZ_CP014971.2_1196739_1198023_-	COG3950, COG3950, Predicted ATP-binding protein involved in virulence [General function prediction only]	NA|690aa|down_0|NZ_CP014971.2_1198525_1200595_-	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|72aa|down_1|NZ_CP014971.2_1200630_1200846_-	COG3311, AlpA, Predicted transcriptional regulator [Transcription]	NA|276aa|down_2|NZ_CP014971.2_1201296_1202124_+	NA	NA|398aa|down_3|NZ_CP014971.2_1202458_1203652_-	pfam02810, SEC-C, SEC-C motif	NA|198aa|down_4|NZ_CP014971.2_1204041_1204635_-	NA	NA|388aa|down_5|NZ_CP014971.2_1206527_1207691_-	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family	NA|727aa|down_6|NZ_CP014971.2_1207698_1209879_-	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family	NA|470aa|down_7|NZ_CP014971.2_1209875_1211285_-	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family	NA|3825aa|down_8|NZ_CP014971.2_1211349_1222824_-	pfam17936, Big_6, Bacterial Ig domain	NA|161aa|down_9|NZ_CP014971.2_1223437_1223920_-	PRK05422, smpB, SsrA-binding protein SmpB
GCF_001623765.2_ASM162376v2	NZ_CP014974	Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1898 isolate ST073 plasmid pSTY3-1898, complete sequence	1	252-371	1	CRISPRCasFinder	no			Orphan	TGAAAGGTGGATGGGTACGCACTGAAAGGTGGATGGGTACGCA	43	0	0	NA	NA	NA	1	1	Orphan	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG	NA,NA|149aa|down_1|NZ_CP014974.1_1499_1946_+,NA|118aa|down_2|NZ_CP014974.1_2082_2436_+,NA|207aa|down_3|NZ_CP014974.1_3125_3746_-,NA|104aa|down_4|NZ_CP014974.1_3783_4095_-,NA|310aa|down_8|NZ_CP014974.1_6464_7394_+,NA|60aa|down_9|NZ_CP014974.1_7734_7914_-	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|279aa|down_0|NZ_CP014974.1_623_1460_+	pfam01051, Rep_3, Initiator Replication protein	NA|149aa|down_1|NZ_CP014974.1_1499_1946_+	NA	NA|118aa|down_2|NZ_CP014974.1_2082_2436_+	NA	NA|207aa|down_3|NZ_CP014974.1_3125_3746_-	NA	NA|104aa|down_4|NZ_CP014974.1_3783_4095_-	NA	NA|77aa|down_5|NZ_CP014974.1_4110_4341_-	pfam09274, ParG, ParG	NA|207aa|down_6|NZ_CP014974.1_4392_5013_-	cd02042, ParAB_family, partition proteins ParAB family	NA|215aa|down_7|NZ_CP014974.1_5298_5943_+	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|310aa|down_8|NZ_CP014974.1_6464_7394_+	NA	NA|60aa|down_9|NZ_CP014974.1_7734_7914_-	NA
