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_001623805.1_ASM162380v1	NZ_CP014975	Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2009K-1640 isolate USDA-ARS-USMARC-1906 chromosome, complete genome	1	680876-680976	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_CP014975.1_682494_683025_-	NA|448aa|up_9|NZ_CP014975.1_666954_668298_-	PRK05370, PRK05370, argininosuccinate synthase; Validated	NA|151aa|up_8|NZ_CP014975.1_668925_669378_+	PRK00092, PRK00092, ribosome maturation protein RimP; Reviewed	NA|501aa|up_7|NZ_CP014975.1_669405_670908_+	PRK09202, nusA, transcription elongation factor NusA; Validated	NA|893aa|up_6|NZ_CP014975.1_670932_673611_+	PRK05306, infB, translation initiation factor IF-2; Validated	NA|134aa|up_5|NZ_CP014975.1_673831_674233_+	PRK00521, rbfA, 30S ribosome-binding factor RbfA	NA|315aa|up_4|NZ_CP014975.1_674232_675177_+	PRK05033, truB, tRNA pseudouridine synthase B; Provisional	NA|90aa|up_3|NZ_CP014975.1_675327_675597_+	PRK05626, rpsO, 30S ribosomal protein S15; Reviewed	NA|712aa|up_2|NZ_CP014975.1_675838_677974_+	PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional	NA|295aa|up_1|NZ_CP014975.1_678083_678968_+	PRK11189, PRK11189, lipoprotein NlpI; Provisional	NA|27aa|up_0|NZ_CP014975.1_679073_679154_+	NF033440, small_YrbN, protein YrbN	NA|415aa|down_0|NZ_CP014975.1_681189_682434_+	PRK10483, PRK10483, tryptophan permease; Provisional	NA|177aa|down_1|NZ_CP014975.1_682494_683025_-	NA	NA|240aa|down_2|NZ_CP014975.1_683183_683903_+	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown]	NA|336aa|down_3|NZ_CP014975.1_683880_684888_-	PRK10508, PRK10508, luciferase-like monooxygenase	NA|299aa|down_4|NZ_CP014975.1_685065_685962_-	PRK15447, PRK15447, putative protease; Provisional	NA|332aa|down_5|NZ_CP014975.1_685952_686948_-	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|175aa|down_6|NZ_CP014975.1_687164_687689_+	COG3154, COG3154, Putative lipid carrier protein [Lipid metabolism]	NA|168aa|down_7|NZ_CP014975.1_687682_688186_+	COG3153, COG3153, Predicted acetyltransferase [General function prediction only]	NA|106aa|down_8|NZ_CP014975.1_688172_688490_-	PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated	NA|148aa|down_9|NZ_CP014975.1_688527_688971_+	PRK03467, PRK03467, hypothetical protein; Provisional
GCF_001623805.1_ASM162380v1	NZ_CP014975	Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2009K-1640 isolate USDA-ARS-USMARC-1906 chromosome, complete genome	2	1030259-1031873	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,DEDDh,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	25,26,26	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_CP014975.1_1016057_1017200_+	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism]	NA|919aa|up_8|NZ_CP014975.1_1017243_1020000_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|432aa|up_7|NZ_CP014975.1_1020057_1021353_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_6|NZ_CP014975.1_1021404_1023639_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|119aa|up_5|NZ_CP014975.1_1023722_1024079_+	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]	NA|99aa|up_4|NZ_CP014975.1_1024044_1024341_+	COG3668, ParE, Plasmid stabilization system protein [General function prediction only]	NA|267aa|up_3|NZ_CP014975.1_1025108_1025909_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|NZ_CP014975.1_1026136_1027774_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|NZ_CP014975.1_1027856_1029155_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|NZ_CP014975.1_1029290_1029962_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|NZ_CP014975.1_1031970_1032768_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|NZ_CP014975.1_1032855_1033218_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|600aa|down_2|NZ_CP014975.1_1033641_1035441_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_3|NZ_CP014975.1_1035440_1037153_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_4|NZ_CP014975.1_1037228_1037963_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_5|NZ_CP014975.1_1038050_1039004_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|down_6|NZ_CP014975.1_1039448_1042112_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|down_7|NZ_CP014975.1_1042123_1043680_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|down_8|NZ_CP014975.1_1043676_1044237_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|down_9|NZ_CP014975.1_1044250_1045309_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI
GCF_001623805.1_ASM162380v1	NZ_CP014975	Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2009K-1640 isolate USDA-ARS-USMARC-1906 chromosome, complete genome	3	1048005-1048643	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,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_CP014975.1_1037228_1037963_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP014975.1_1038050_1039004_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP014975.1_1039448_1042112_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP014975.1_1042123_1043680_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP014975.1_1043676_1044237_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP014975.1_1044250_1045309_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP014975.1_1045319_1046066_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP014975.1_1046047_1046698_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP014975.1_1046694_1047615_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP014975.1_1047614_1047908_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP014975.1_1048657_1049704_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP014975.1_1049954_1050863_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP014975.1_1050872_1052312_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP014975.1_1052298_1052904_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP014975.1_1052954_1053278_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP014975.1_1053468_1053780_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP014975.1_1053798_1054509_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP014975.1_1054508_1054988_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP014975.1_1054984_1056034_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP014975.1_1056014_1056776_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_001623805.1_ASM162380v1	NZ_CP014975	Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2009K-1640 isolate USDA-ARS-USMARC-1906 chromosome, complete genome	4	1239560-1239669	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_CP014975.1_1242457_1243285_+,NA|198aa|down_4|NZ_CP014975.1_1245202_1245796_-	NA|281aa|up_9|NZ_CP014975.1_1229507_1230350_+	pfam06560, GPI, Glucose-6-phosphate isomerase (GPI)	NA|188aa|up_8|NZ_CP014975.1_1230349_1230913_+	TIGR03127, RuMP_HxlB, 6-phospho 3-hexuloisomerase	NA|212aa|up_7|NZ_CP014975.1_1230936_1231572_+	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase	NA|338aa|up_6|NZ_CP014975.1_1233141_1234155_-	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|327aa|up_5|NZ_CP014975.1_1234165_1235146_-	COG3732, SrlE, Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism]	NA|125aa|up_4|NZ_CP014975.1_1235142_1235517_-	COG3731, SrlB, Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]	NA|174aa|up_3|NZ_CP014975.1_1235513_1236035_-	COG3730, SrlA, Phosphotransferase system sorbitol-specific component IIC [Carbohydrate transport and metabolism]	NA|95aa|up_2|NZ_CP014975.1_1236147_1236432_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|119aa|up_1|NZ_CP014975.1_1236526_1236883_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|273aa|up_0|NZ_CP014975.1_1237036_1237855_-	pfam14491, DUF4435, Protein of unknown function (DUF4435)	NA|690aa|down_0|NZ_CP014975.1_1239686_1241756_-	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|72aa|down_1|NZ_CP014975.1_1241791_1242007_-	COG3311, AlpA, Predicted transcriptional regulator [Transcription]	NA|276aa|down_2|NZ_CP014975.1_1242457_1243285_+	NA	NA|398aa|down_3|NZ_CP014975.1_1243619_1244813_-	pfam02810, SEC-C, SEC-C motif	NA|198aa|down_4|NZ_CP014975.1_1245202_1245796_-	NA	NA|388aa|down_5|NZ_CP014975.1_1247688_1248852_-	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family	NA|727aa|down_6|NZ_CP014975.1_1248859_1251040_-	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family	NA|470aa|down_7|NZ_CP014975.1_1251036_1252446_-	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family	NA|3825aa|down_8|NZ_CP014975.1_1252510_1263985_-	pfam17936, Big_6, Bacterial Ig domain	NA|161aa|down_9|NZ_CP014975.1_1264598_1265081_-	PRK05422, smpB, SsrA-binding protein SmpB
