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
GCA_003994655.1_ASM399465v1	CP034719	Salmonella enterica subsp. enterica serovar Typhimurium strain RSE04 chromosome, complete genome	2	948581-950562	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	31,32,32	32	TypeI-E	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,RT,cas14j	NA,NA|57aa|down_2|CP034719.1_951835_952006_+,NA|75aa|down_7|CP034719.1_957808_958033_-	NA|381aa|up_9|CP034719.1_934379_935522_+	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism]	NA|919aa|up_8|CP034719.1_935565_938322_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|432aa|up_7|CP034719.1_938379_939675_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_6|CP034719.1_939726_941961_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|119aa|up_5|CP034719.1_942044_942401_+	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]	NA|99aa|up_4|CP034719.1_942366_942663_+	COG3668, ParE, Plasmid stabilization system protein [General function prediction only]	NA|267aa|up_3|CP034719.1_943430_944231_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|CP034719.1_944458_946096_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|CP034719.1_946178_947477_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|CP034719.1_947612_948284_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|CP034719.1_950659_951457_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|CP034719.1_951544_951907_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|57aa|down_2|CP034719.1_951835_952006_+	NA	NA|600aa|down_3|CP034719.1_952330_954130_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_4|CP034719.1_954129_955842_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_5|CP034719.1_955917_956652_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_6|CP034719.1_956739_957693_-	PRK15379, PRK15379, type III secretion system effector SopD	NA|75aa|down_7|CP034719.1_957808_958033_-	NA	cas3|888aa|down_8|CP034719.1_958137_960801_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|down_9|CP034719.1_960812_962369_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1
GCA_003994655.1_ASM399465v1	CP034719	Salmonella enterica subsp. enterica serovar Typhimurium strain RSE04 chromosome, complete genome	3	966694-967701	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	15,16,16	16	TypeI-E	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,RT,cas14j	NA|75aa|up_8|CP034719.1_957808_958033_-,NA	NA|318aa|up_9|CP034719.1_956739_957693_-	PRK15379, PRK15379, type III secretion system effector SopD	NA|75aa|up_8|CP034719.1_957808_958033_-	NA	cas3|888aa|up_7|CP034719.1_958137_960801_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|CP034719.1_960812_962369_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|CP034719.1_962365_962926_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|CP034719.1_962939_963998_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|CP034719.1_964008_964755_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|CP034719.1_964736_965387_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|CP034719.1_965383_966304_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|CP034719.1_966303_966597_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|CP034719.1_968366_969413_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|CP034719.1_969663_970572_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|CP034719.1_970581_972021_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|CP034719.1_972007_972613_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|119aa|down_4|CP034719.1_972630_972987_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|CP034719.1_973177_973489_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|CP034719.1_973507_974218_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|CP034719.1_974217_974697_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|CP034719.1_974693_975743_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|CP034719.1_975723_976485_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCA_003994655.1_ASM399465v1	CP034719	Salmonella enterica subsp. enterica serovar Typhimurium strain RSE04 chromosome, complete genome	4	967775-968352	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|75aa|up_8|CP034719.1_957808_958033_-,NA	NA|318aa|up_9|CP034719.1_956739_957693_-	PRK15379, PRK15379, type III secretion system effector SopD	NA|75aa|up_8|CP034719.1_957808_958033_-	NA	cas3|888aa|up_7|CP034719.1_958137_960801_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|CP034719.1_960812_962369_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|CP034719.1_962365_962926_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|CP034719.1_962939_963998_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|CP034719.1_964008_964755_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|CP034719.1_964736_965387_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|CP034719.1_965383_966304_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|CP034719.1_966303_966597_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|CP034719.1_968366_969413_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|CP034719.1_969663_970572_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|CP034719.1_970581_972021_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|CP034719.1_972007_972613_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|119aa|down_4|CP034719.1_972630_972987_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|CP034719.1_973177_973489_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|CP034719.1_973507_974218_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|CP034719.1_974217_974697_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|CP034719.1_974693_975743_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|CP034719.1_975723_976485_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCA_003994655.1_ASM399465v1	CP034719	Salmonella enterica subsp. enterica serovar Typhimurium strain RSE04 chromosome, complete genome	5	1159269-1159378	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|CP034719.1_1162166_1162994_+,NA|198aa|down_4|CP034719.1_1164911_1165505_-	NA|212aa|up_9|CP034719.1_1150645_1151281_+	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase	NA|401aa|up_8|CP034719.1_1151354_1152557_-	pfam13020, DUF3883, Domain of unknown function (DUF3883)	NA|338aa|up_7|CP034719.1_1152851_1153865_-	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|327aa|up_6|CP034719.1_1153875_1154856_-	COG3732, SrlE, Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism]	NA|125aa|up_5|CP034719.1_1154852_1155227_-	COG3731, SrlB, Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]	NA|174aa|up_4|CP034719.1_1155223_1155745_-	COG3730, SrlA, Phosphotransferase system sorbitol-specific component IIC [Carbohydrate transport and metabolism]	NA|95aa|up_3|CP034719.1_1155857_1156142_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|119aa|up_2|CP034719.1_1156236_1156593_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|273aa|up_1|CP034719.1_1156746_1157565_-	pfam14491, DUF4435, Protein of unknown function (DUF4435)	NA|428aa|up_0|CP034719.1_1157609_1158893_-	COG3950, COG3950, Predicted ATP-binding protein involved in virulence [General function prediction only]	NA|690aa|down_0|CP034719.1_1159395_1161465_-	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|72aa|down_1|CP034719.1_1161500_1161716_-	COG3311, AlpA, Predicted transcriptional regulator [Transcription]	NA|276aa|down_2|CP034719.1_1162166_1162994_+	NA	NA|398aa|down_3|CP034719.1_1163328_1164522_-	pfam02810, SEC-C, SEC-C motif	NA|198aa|down_4|CP034719.1_1164911_1165505_-	NA	NA|56aa|down_5|CP034719.1_1165551_1165719_-	PRK09692, PRK09692, integrase; Provisional	NA|355aa|down_6|CP034719.1_1165732_1166797_-	PRK09692, PRK09692, integrase; Provisional	NA|388aa|down_7|CP034719.1_1167397_1168561_-	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family	NA|727aa|down_8|CP034719.1_1168568_1170749_-	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family	NA|470aa|down_9|CP034719.1_1170745_1172155_-	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family
