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_009664595.1_ASM966459v1	NZ_CP045949	Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00010529 chromosome, complete genome	1	599289-599389	1	CRISPRCasFinder	no		cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG,RT	Orphan	GCTTCAGTGGCGAACGTCGTGAA	23	0	0	NA	NA	NA	1	1	Orphan	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG,RT,c2c9_V-U4	NA,NA|177aa|down_1|NZ_CP045949.1_600907_601438_-	NA|448aa|up_9|NZ_CP045949.1_585367_586711_-	PRK05370, PRK05370, argininosuccinate synthase; Validated	NA|151aa|up_8|NZ_CP045949.1_587338_587791_+	PRK00092, PRK00092, ribosome maturation protein RimP; Reviewed	NA|501aa|up_7|NZ_CP045949.1_587818_589321_+	PRK09202, nusA, transcription elongation factor NusA; Validated	NA|893aa|up_6|NZ_CP045949.1_589345_592024_+	PRK05306, infB, translation initiation factor IF-2; Validated	NA|134aa|up_5|NZ_CP045949.1_592244_592646_+	PRK00521, rbfA, 30S ribosome-binding factor RbfA	NA|315aa|up_4|NZ_CP045949.1_592645_593590_+	PRK05033, truB, tRNA pseudouridine synthase B; Provisional	NA|90aa|up_3|NZ_CP045949.1_593740_594010_+	PRK05626, rpsO, 30S ribosomal protein S15; Reviewed	NA|712aa|up_2|NZ_CP045949.1_594251_596387_+	PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional	NA|295aa|up_1|NZ_CP045949.1_596496_597381_+	PRK11189, PRK11189, lipoprotein NlpI; Provisional	NA|27aa|up_0|NZ_CP045949.1_597486_597567_+	NF033440, small_YrbN, protein YrbN	NA|415aa|down_0|NZ_CP045949.1_599602_600847_+	PRK10483, PRK10483, tryptophan permease; Provisional	NA|177aa|down_1|NZ_CP045949.1_600907_601438_-	NA	NA|240aa|down_2|NZ_CP045949.1_601596_602316_+	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown]	NA|336aa|down_3|NZ_CP045949.1_602293_603301_-	PRK10508, PRK10508, luciferase-like monooxygenase	NA|299aa|down_4|NZ_CP045949.1_603478_604375_-	PRK15447, PRK15447, putative protease; Provisional	NA|332aa|down_5|NZ_CP045949.1_604365_605361_-	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|175aa|down_6|NZ_CP045949.1_605577_606102_+	COG3154, COG3154, Putative lipid carrier protein [Lipid metabolism]	NA|168aa|down_7|NZ_CP045949.1_606095_606599_+	COG3153, COG3153, Predicted acetyltransferase [General function prediction only]	NA|106aa|down_8|NZ_CP045949.1_606585_606903_-	PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated	NA|148aa|down_9|NZ_CP045949.1_606940_607384_+	PRK03467, PRK03467, hypothetical protein; Provisional
GCF_009664595.1_ASM966459v1	NZ_CP045949	Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00010529 chromosome, complete genome	2	949335-950646	1,2,1,2	PILER-CR,CRISPRCasFinder,CRT,PILER-CR	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG,RT	Type I-E	TCGTGTTCCCCGCGCCAGCGGGGATAAACCGTT,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	33,29,29,29	0	0	NA	NA	I-E:I-E:I-E:I-E	18,21,21,18	21	TypeI-E	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG,RT,c2c9_V-U4	NA,NA	NA|381aa|up_9|NZ_CP045949.1_935134_936277_+	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism]	NA|919aa|up_8|NZ_CP045949.1_936320_939077_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|432aa|up_7|NZ_CP045949.1_939134_940430_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_6|NZ_CP045949.1_940481_942716_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|119aa|up_5|NZ_CP045949.1_942799_943156_+	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]	NA|99aa|up_4|NZ_CP045949.1_943121_943418_+	COG3668, ParE, Plasmid stabilization system protein [General function prediction only]	NA|267aa|up_3|NZ_CP045949.1_944185_944986_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|NZ_CP045949.1_945213_946851_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|NZ_CP045949.1_946933_948232_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|NZ_CP045949.1_948367_949039_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|NZ_CP045949.1_950743_951541_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|NZ_CP045949.1_951628_951991_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|600aa|down_2|NZ_CP045949.1_952414_954214_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_3|NZ_CP045949.1_954213_955926_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_4|NZ_CP045949.1_956001_956736_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_5|NZ_CP045949.1_956823_957777_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|down_6|NZ_CP045949.1_958221_960885_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|down_7|NZ_CP045949.1_960896_962453_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|down_8|NZ_CP045949.1_962449_963010_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|down_9|NZ_CP045949.1_963023_964082_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI
GCF_009664595.1_ASM966459v1	NZ_CP045949	Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00010529 chromosome, complete genome	3	966778-967052	3,3,2	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG,RT	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	3,4,4	4	TypeI-E	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG,RT,c2c9_V-U4	NA,NA	NA|245aa|up_9|NZ_CP045949.1_956001_956736_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP045949.1_956823_957777_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP045949.1_958221_960885_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP045949.1_960896_962453_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP045949.1_962449_963010_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP045949.1_963023_964082_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP045949.1_964092_964839_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP045949.1_964820_965471_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP045949.1_965467_966388_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP045949.1_966387_966681_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP045949.1_967717_968764_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP045949.1_969014_969923_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP045949.1_969932_971372_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP045949.1_971358_971964_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|119aa|down_4|NZ_CP045949.1_971981_972338_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP045949.1_972528_972840_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP045949.1_972858_973569_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP045949.1_973568_974048_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP045949.1_974044_975094_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP045949.1_975074_975836_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_009664595.1_ASM966459v1	NZ_CP045949	Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00010529 chromosome, complete genome	4	967126-967703	4,4,3	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG,RT	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	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG,RT,c2c9_V-U4	NA,NA	NA|245aa|up_9|NZ_CP045949.1_956001_956736_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP045949.1_956823_957777_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP045949.1_958221_960885_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP045949.1_960896_962453_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP045949.1_962449_963010_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP045949.1_963023_964082_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP045949.1_964092_964839_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP045949.1_964820_965471_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP045949.1_965467_966388_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP045949.1_966387_966681_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP045949.1_967717_968764_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP045949.1_969014_969923_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP045949.1_969932_971372_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP045949.1_971358_971964_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|119aa|down_4|NZ_CP045949.1_971981_972338_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP045949.1_972528_972840_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP045949.1_972858_973569_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP045949.1_973568_974048_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP045949.1_974044_975094_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP045949.1_975074_975836_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_009664595.1_ASM966459v1	NZ_CP045949	Salmonella enterica subsp. enterica serovar Typhimurium strain AUSMDU00010529 chromosome, complete genome	5	1158629-1158738	5	CRISPRCasFinder	no		cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG,RT	Orphan	TGTCCCACCCTGTACCACTTTTTTTTAA	28	0	0	NA	NA	NA	1	1	Orphan	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,cas14j,DEDDh,DinG,RT,c2c9_V-U4	NA,NA|276aa|down_2|NZ_CP045949.1_1161526_1162354_+,NA|198aa|down_4|NZ_CP045949.1_1164271_1164865_-,NA|76aa|down_9|NZ_CP045949.1_1169313_1169541_-	NA|212aa|up_9|NZ_CP045949.1_1150005_1150641_+	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase	NA|401aa|up_8|NZ_CP045949.1_1150714_1151917_-	pfam13020, DUF3883, Domain of unknown function (DUF3883)	NA|338aa|up_7|NZ_CP045949.1_1152211_1153225_-	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|327aa|up_6|NZ_CP045949.1_1153235_1154216_-	COG3732, SrlE, Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism]	NA|125aa|up_5|NZ_CP045949.1_1154212_1154587_-	COG3731, SrlB, Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]	NA|174aa|up_4|NZ_CP045949.1_1154583_1155105_-	COG3730, SrlA, Phosphotransferase system sorbitol-specific component IIC [Carbohydrate transport and metabolism]	NA|95aa|up_3|NZ_CP045949.1_1155217_1155502_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|119aa|up_2|NZ_CP045949.1_1155596_1155953_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|273aa|up_1|NZ_CP045949.1_1156106_1156925_-	pfam14491, DUF4435, Protein of unknown function (DUF4435)	NA|428aa|up_0|NZ_CP045949.1_1156969_1158253_-	COG3950, COG3950, Predicted ATP-binding protein involved in virulence [General function prediction only]	NA|690aa|down_0|NZ_CP045949.1_1158755_1160825_-	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|72aa|down_1|NZ_CP045949.1_1160860_1161076_-	COG3311, AlpA, Predicted transcriptional regulator [Transcription]	NA|276aa|down_2|NZ_CP045949.1_1161526_1162354_+	NA	NA|398aa|down_3|NZ_CP045949.1_1162688_1163882_-	pfam02810, SEC-C, SEC-C motif	NA|198aa|down_4|NZ_CP045949.1_1164271_1164865_-	NA	NA|56aa|down_5|NZ_CP045949.1_1164911_1165079_-	PRK09692, PRK09692, integrase; Provisional	NA|355aa|down_6|NZ_CP045949.1_1165092_1166157_-	PRK09692, PRK09692, integrase; Provisional	NA|778aa|down_7|NZ_CP045949.1_1166648_1168982_-	COG3378, COG3378, Phage associated DNA primase [General function prediction only]	NA|107aa|down_8|NZ_CP045949.1_1168996_1169317_-	pfam17345, DUF5375, Family of unknown function (DUF5375)	NA|76aa|down_9|NZ_CP045949.1_1169313_1169541_-	NA
