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_007923125.1_ASM792312v1	NZ_CP035301	Salmonella enterica subsp. enterica strain ST1539 chromosome, complete genome	1	599841-599941	1	CRISPRCasFinder	no		cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,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,DEDDh,DinG,RT,cas14j	NA,NA|177aa|down_1|NZ_CP035301.1_601459_601990_-	NA|448aa|up_9|NZ_CP035301.1_585919_587263_-	PRK05370, PRK05370, argininosuccinate synthase; Validated	NA|151aa|up_8|NZ_CP035301.1_587890_588343_+	PRK00092, PRK00092, ribosome maturation protein RimP; Reviewed	NA|501aa|up_7|NZ_CP035301.1_588370_589873_+	PRK09202, nusA, transcription elongation factor NusA; Validated	NA|893aa|up_6|NZ_CP035301.1_589897_592576_+	PRK05306, infB, translation initiation factor IF-2; Validated	NA|134aa|up_5|NZ_CP035301.1_592796_593198_+	PRK00521, rbfA, 30S ribosome-binding factor RbfA	NA|315aa|up_4|NZ_CP035301.1_593197_594142_+	PRK05033, truB, tRNA pseudouridine synthase B; Provisional	NA|90aa|up_3|NZ_CP035301.1_594292_594562_+	PRK05626, rpsO, 30S ribosomal protein S15; Reviewed	NA|712aa|up_2|NZ_CP035301.1_594803_596939_+	PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional	NA|295aa|up_1|NZ_CP035301.1_597048_597933_+	PRK11189, PRK11189, lipoprotein NlpI; Provisional	NA|27aa|up_0|NZ_CP035301.1_598038_598119_+	NF033440, small_YrbN, protein YrbN	NA|415aa|down_0|NZ_CP035301.1_600154_601399_+	PRK10483, PRK10483, tryptophan permease; Provisional	NA|177aa|down_1|NZ_CP035301.1_601459_601990_-	NA	NA|240aa|down_2|NZ_CP035301.1_602148_602868_+	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown]	NA|336aa|down_3|NZ_CP035301.1_602845_603853_-	PRK10508, PRK10508, luciferase-like monooxygenase	NA|299aa|down_4|NZ_CP035301.1_604030_604927_-	PRK15447, PRK15447, putative protease; Provisional	NA|332aa|down_5|NZ_CP035301.1_604917_605913_-	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|175aa|down_6|NZ_CP035301.1_606129_606654_+	COG3154, COG3154, Putative lipid carrier protein [Lipid metabolism]	NA|168aa|down_7|NZ_CP035301.1_606647_607151_+	COG3153, COG3153, Predicted acetyltransferase [General function prediction only]	NA|106aa|down_8|NZ_CP035301.1_607137_607455_-	PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated	NA|148aa|down_9|NZ_CP035301.1_607492_607936_+	PRK03467, PRK03467, hypothetical protein; Provisional
GCF_007923125.1_ASM792312v1	NZ_CP035301	Salmonella enterica subsp. enterica strain ST1539 chromosome, complete genome	2	949183-949760	1,2,1	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,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,DEDDh,DinG,RT,cas14j	NA,NA	NA|381aa|up_9|NZ_CP035301.1_934981_936124_+	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism]	NA|919aa|up_8|NZ_CP035301.1_936167_938924_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|432aa|up_7|NZ_CP035301.1_938981_940277_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_6|NZ_CP035301.1_940328_942563_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|119aa|up_5|NZ_CP035301.1_942646_943003_+	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]	NA|99aa|up_4|NZ_CP035301.1_942968_943265_+	COG3668, ParE, Plasmid stabilization system protein [General function prediction only]	NA|267aa|up_3|NZ_CP035301.1_944032_944833_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|NZ_CP035301.1_945060_946698_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|NZ_CP035301.1_946780_948079_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|NZ_CP035301.1_948214_948886_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|NZ_CP035301.1_949857_950655_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|NZ_CP035301.1_950742_951105_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|600aa|down_2|NZ_CP035301.1_951528_953328_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_3|NZ_CP035301.1_953327_955040_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_4|NZ_CP035301.1_955115_955850_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_5|NZ_CP035301.1_955937_956891_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|down_6|NZ_CP035301.1_957335_959999_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|down_7|NZ_CP035301.1_960010_961567_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|down_8|NZ_CP035301.1_961563_962124_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|down_9|NZ_CP035301.1_962137_963196_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI
GCF_007923125.1_ASM792312v1	NZ_CP035301	Salmonella enterica subsp. enterica strain ST1539 chromosome, complete genome	3	965892-966716	2,3,2	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,DEDDh,DinG,RT	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	12,13,13	13	TypeI-E	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,RT,cas14j	NA,NA	NA|245aa|up_9|NZ_CP035301.1_955115_955850_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP035301.1_955937_956891_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP035301.1_957335_959999_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP035301.1_960010_961567_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP035301.1_961563_962124_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP035301.1_962137_963196_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP035301.1_963206_963953_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP035301.1_963934_964585_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP035301.1_964581_965502_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP035301.1_965501_965795_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP035301.1_967381_968428_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP035301.1_968678_969587_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP035301.1_969596_971036_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP035301.1_971022_971628_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|104aa|down_4|NZ_CP035301.1_972191_972503_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_5|NZ_CP035301.1_972521_973232_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_6|NZ_CP035301.1_973231_973711_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_7|NZ_CP035301.1_973707_974757_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_8|NZ_CP035301.1_974737_975499_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional	NA|209aa|down_9|NZ_CP035301.1_975492_976119_+	PRK00312, pcm, protein-L-isoaspartate(D-aspartate) O-methyltransferase
GCF_007923125.1_ASM792312v1	NZ_CP035301	Salmonella enterica subsp. enterica strain ST1539 chromosome, complete genome	4	966790-967367	3,4,3	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,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,DEDDh,DinG,RT,cas14j	NA,NA	NA|245aa|up_9|NZ_CP035301.1_955115_955850_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP035301.1_955937_956891_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP035301.1_957335_959999_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP035301.1_960010_961567_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP035301.1_961563_962124_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP035301.1_962137_963196_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP035301.1_963206_963953_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP035301.1_963934_964585_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP035301.1_964581_965502_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP035301.1_965501_965795_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP035301.1_967381_968428_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP035301.1_968678_969587_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP035301.1_969596_971036_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP035301.1_971022_971628_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|104aa|down_4|NZ_CP035301.1_972191_972503_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_5|NZ_CP035301.1_972521_973232_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_6|NZ_CP035301.1_973231_973711_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_7|NZ_CP035301.1_973707_974757_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_8|NZ_CP035301.1_974737_975499_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional	NA|209aa|down_9|NZ_CP035301.1_975492_976119_+	PRK00312, pcm, protein-L-isoaspartate(D-aspartate) O-methyltransferase
GCF_007923125.1_ASM792312v1	NZ_CP035301	Salmonella enterica subsp. enterica strain ST1539 chromosome, complete genome	5	1158282-1158391	5	CRISPRCasFinder	no		cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,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,DEDDh,DinG,RT,cas14j	NA,NA|276aa|down_2|NZ_CP035301.1_1161179_1162007_+,NA|198aa|down_4|NZ_CP035301.1_1163924_1164518_-,NA|221aa|down_7|NZ_CP035301.1_1166140_1166803_-	NA|212aa|up_9|NZ_CP035301.1_1149658_1150294_+	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase	NA|401aa|up_8|NZ_CP035301.1_1150367_1151570_-	pfam13020, DUF3883, Domain of unknown function (DUF3883)	NA|338aa|up_7|NZ_CP035301.1_1151864_1152878_-	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|327aa|up_6|NZ_CP035301.1_1152888_1153869_-	COG3732, SrlE, Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism]	NA|125aa|up_5|NZ_CP035301.1_1153865_1154240_-	COG3731, SrlB, Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]	NA|174aa|up_4|NZ_CP035301.1_1154236_1154758_-	COG3730, SrlA, Phosphotransferase system sorbitol-specific component IIC [Carbohydrate transport and metabolism]	NA|95aa|up_3|NZ_CP035301.1_1154870_1155155_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|119aa|up_2|NZ_CP035301.1_1155249_1155606_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|273aa|up_1|NZ_CP035301.1_1155759_1156578_-	pfam14491, DUF4435, Protein of unknown function (DUF4435)	NA|428aa|up_0|NZ_CP035301.1_1156622_1157906_-	COG3950, COG3950, Predicted ATP-binding protein involved in virulence [General function prediction only]	NA|690aa|down_0|NZ_CP035301.1_1158408_1160478_-	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|72aa|down_1|NZ_CP035301.1_1160513_1160729_-	COG3311, AlpA, Predicted transcriptional regulator [Transcription]	NA|276aa|down_2|NZ_CP035301.1_1161179_1162007_+	NA	NA|398aa|down_3|NZ_CP035301.1_1162341_1163535_-	pfam02810, SEC-C, SEC-C motif	NA|198aa|down_4|NZ_CP035301.1_1163924_1164518_-	NA	NA|56aa|down_5|NZ_CP035301.1_1164564_1164732_-	PRK09692, PRK09692, integrase; Provisional	NA|355aa|down_6|NZ_CP035301.1_1164745_1165810_-	PRK09692, PRK09692, integrase; Provisional	NA|221aa|down_7|NZ_CP035301.1_1166140_1166803_-	NA	NA|339aa|down_8|NZ_CP035301.1_1167355_1168372_-	PHA02601, int, integrase; Provisional	NA|211aa|down_9|NZ_CP035301.1_1168374_1169007_-	pfam07022, Phage_CI_repr, Bacteriophage CI repressor helix-turn-helix domain
