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_001623725.1_ASM162372v1	NZ_CP014969	Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1808 isolate ST1126-1 chromosome, complete genome	1	684232-684332	1	CRISPRCasFinder	no		RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,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,DEDDh,DinG,cas14j	NA,NA|177aa|down_1|NZ_CP014969.1_685850_686381_-	NA|448aa|up_9|NZ_CP014969.1_670310_671654_-	PRK05370, PRK05370, argininosuccinate synthase; Validated	NA|151aa|up_8|NZ_CP014969.1_672281_672734_+	PRK00092, PRK00092, ribosome maturation protein RimP; Reviewed	NA|501aa|up_7|NZ_CP014969.1_672761_674264_+	PRK09202, nusA, transcription elongation factor NusA; Validated	NA|893aa|up_6|NZ_CP014969.1_674288_676967_+	PRK05306, infB, translation initiation factor IF-2; Validated	NA|134aa|up_5|NZ_CP014969.1_677187_677589_+	PRK00521, rbfA, 30S ribosome-binding factor RbfA	NA|315aa|up_4|NZ_CP014969.1_677588_678533_+	PRK05033, truB, tRNA pseudouridine synthase B; Provisional	NA|90aa|up_3|NZ_CP014969.1_678683_678953_+	PRK05626, rpsO, 30S ribosomal protein S15; Reviewed	NA|712aa|up_2|NZ_CP014969.1_679194_681330_+	PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional	NA|295aa|up_1|NZ_CP014969.1_681439_682324_+	PRK11189, PRK11189, lipoprotein NlpI; Provisional	NA|27aa|up_0|NZ_CP014969.1_682429_682510_+	NF033440, small_YrbN, protein YrbN	NA|415aa|down_0|NZ_CP014969.1_684545_685790_+	PRK10483, PRK10483, tryptophan permease; Provisional	NA|177aa|down_1|NZ_CP014969.1_685850_686381_-	NA	NA|240aa|down_2|NZ_CP014969.1_686539_687259_+	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown]	NA|336aa|down_3|NZ_CP014969.1_687236_688244_-	PRK10508, PRK10508, luciferase-like monooxygenase	NA|299aa|down_4|NZ_CP014969.1_688421_689318_-	PRK15447, PRK15447, putative protease; Provisional	NA|332aa|down_5|NZ_CP014969.1_689308_690304_-	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|175aa|down_6|NZ_CP014969.1_690520_691045_+	COG3154, COG3154, Putative lipid carrier protein [Lipid metabolism]	NA|168aa|down_7|NZ_CP014969.1_691038_691542_+	COG3153, COG3153, Predicted acetyltransferase [General function prediction only]	NA|106aa|down_8|NZ_CP014969.1_691528_691846_-	PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated	NA|148aa|down_9|NZ_CP014969.1_691883_692327_+	PRK03467, PRK03467, hypothetical protein; Provisional
GCF_001623725.1_ASM162372v1	NZ_CP014969	Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1808 isolate ST1126-1 chromosome, complete genome	2	1033598-1035212	1,2,1,2	PILER-CR,CRISPRCasFinder,CRT,PILER-CR	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAA	29,29,29,26	0	0	NA	NA	I-E:I-E:I-E:I-E	22,26,26,22	26	TypeI-E	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,cas14j	NA,NA	NA|381aa|up_9|NZ_CP014969.1_1019396_1020539_+	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism]	NA|919aa|up_8|NZ_CP014969.1_1020582_1023339_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|432aa|up_7|NZ_CP014969.1_1023396_1024692_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_6|NZ_CP014969.1_1024743_1026978_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|119aa|up_5|NZ_CP014969.1_1027061_1027418_+	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]	NA|99aa|up_4|NZ_CP014969.1_1027383_1027680_+	COG3668, ParE, Plasmid stabilization system protein [General function prediction only]	NA|267aa|up_3|NZ_CP014969.1_1028447_1029248_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|NZ_CP014969.1_1029475_1031113_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|NZ_CP014969.1_1031195_1032494_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|NZ_CP014969.1_1032629_1033301_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|NZ_CP014969.1_1035309_1036107_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|NZ_CP014969.1_1036194_1036557_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|600aa|down_2|NZ_CP014969.1_1036980_1038780_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_3|NZ_CP014969.1_1038779_1040492_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_4|NZ_CP014969.1_1040567_1041302_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_5|NZ_CP014969.1_1041389_1042343_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|down_6|NZ_CP014969.1_1042787_1045451_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|down_7|NZ_CP014969.1_1045462_1047019_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|down_8|NZ_CP014969.1_1047015_1047576_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|down_9|NZ_CP014969.1_1047589_1048648_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI
GCF_001623725.1_ASM162372v1	NZ_CP014969	Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1808 isolate ST1126-1 chromosome, complete genome	3	1051344-1051982	3,3,2	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,DEDDh,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	9,10,10	10	TypeI-E	RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,cas14j	NA,NA	NA|245aa|up_9|NZ_CP014969.1_1040567_1041302_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP014969.1_1041389_1042343_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP014969.1_1042787_1045451_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP014969.1_1045462_1047019_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP014969.1_1047015_1047576_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP014969.1_1047589_1048648_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP014969.1_1048658_1049405_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP014969.1_1049386_1050037_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP014969.1_1050033_1050954_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP014969.1_1050953_1051247_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP014969.1_1051996_1053043_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP014969.1_1053293_1054202_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP014969.1_1054211_1055651_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP014969.1_1055637_1056243_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP014969.1_1056293_1056617_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP014969.1_1056807_1057119_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP014969.1_1057137_1057848_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP014969.1_1057847_1058327_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP014969.1_1058323_1059373_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP014969.1_1059353_1060115_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_001623725.1_ASM162372v1	NZ_CP014969	Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1808 isolate ST1126-1 chromosome, complete genome	4	1242899-1243008	4	CRISPRCasFinder	no		RT,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,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,DEDDh,DinG,cas14j	NA,NA|276aa|down_2|NZ_CP014969.1_1245796_1246624_+,NA|198aa|down_4|NZ_CP014969.1_1248541_1249135_-	NA|281aa|up_9|NZ_CP014969.1_1232846_1233689_+	pfam06560, GPI, Glucose-6-phosphate isomerase (GPI)	NA|188aa|up_8|NZ_CP014969.1_1233688_1234252_+	TIGR03127, RuMP_HxlB, 6-phospho 3-hexuloisomerase	NA|212aa|up_7|NZ_CP014969.1_1234275_1234911_+	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase	NA|338aa|up_6|NZ_CP014969.1_1236480_1237494_-	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|327aa|up_5|NZ_CP014969.1_1237504_1238485_-	COG3732, SrlE, Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism]	NA|125aa|up_4|NZ_CP014969.1_1238481_1238856_-	COG3731, SrlB, Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]	NA|174aa|up_3|NZ_CP014969.1_1238852_1239374_-	COG3730, SrlA, Phosphotransferase system sorbitol-specific component IIC [Carbohydrate transport and metabolism]	NA|95aa|up_2|NZ_CP014969.1_1239486_1239771_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|119aa|up_1|NZ_CP014969.1_1239865_1240222_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|273aa|up_0|NZ_CP014969.1_1240375_1241194_-	pfam14491, DUF4435, Protein of unknown function (DUF4435)	NA|690aa|down_0|NZ_CP014969.1_1243025_1245095_-	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|72aa|down_1|NZ_CP014969.1_1245130_1245346_-	COG3311, AlpA, Predicted transcriptional regulator [Transcription]	NA|276aa|down_2|NZ_CP014969.1_1245796_1246624_+	NA	NA|398aa|down_3|NZ_CP014969.1_1246958_1248152_-	pfam02810, SEC-C, SEC-C motif	NA|198aa|down_4|NZ_CP014969.1_1248541_1249135_-	NA	NA|388aa|down_5|NZ_CP014969.1_1251027_1252191_-	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family	NA|727aa|down_6|NZ_CP014969.1_1252198_1254379_-	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family	NA|470aa|down_7|NZ_CP014969.1_1254375_1255785_-	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family	NA|3825aa|down_8|NZ_CP014969.1_1255849_1267324_-	pfam17936, Big_6, Bacterial Ig domain	NA|161aa|down_9|NZ_CP014969.1_1267937_1268420_-	PRK05422, smpB, SsrA-binding protein SmpB
