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_003864015.1_ASM386401v1	CP034230	Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 14028 chromosome, complete genome	2	942638-944253	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,cas14j,RT	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	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,cas14j,RT	NA,NA|57aa|down_2|CP034230.1_945526_945697_+,NA|75aa|down_7|CP034230.1_951499_951724_-	NA|381aa|up_9|CP034230.1_928436_929579_+	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism]	NA|919aa|up_8|CP034230.1_929622_932379_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|432aa|up_7|CP034230.1_932436_933732_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_6|CP034230.1_933783_936018_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|119aa|up_5|CP034230.1_936101_936458_+	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]	NA|99aa|up_4|CP034230.1_936423_936720_+	COG3668, ParE, Plasmid stabilization system protein [General function prediction only]	NA|267aa|up_3|CP034230.1_937487_938288_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|CP034230.1_938515_940153_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|CP034230.1_940235_941534_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|CP034230.1_941669_942341_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|CP034230.1_944350_945148_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|CP034230.1_945235_945598_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|57aa|down_2|CP034230.1_945526_945697_+	NA	NA|600aa|down_3|CP034230.1_946021_947821_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_4|CP034230.1_947820_949533_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_5|CP034230.1_949608_950343_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_6|CP034230.1_950430_951384_-	PRK15379, PRK15379, type III secretion system effector SopD	NA|75aa|down_7|CP034230.1_951499_951724_-	NA	cas3|888aa|down_8|CP034230.1_951828_954492_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|down_9|CP034230.1_954503_956060_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1
GCA_003864015.1_ASM386401v1	CP034230	Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 14028 chromosome, complete genome	3	960385-961209	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,cas14j,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,cas14j,RT	NA|75aa|up_8|CP034230.1_951499_951724_-,NA	NA|318aa|up_9|CP034230.1_950430_951384_-	PRK15379, PRK15379, type III secretion system effector SopD	NA|75aa|up_8|CP034230.1_951499_951724_-	NA	cas3|888aa|up_7|CP034230.1_951828_954492_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|CP034230.1_954503_956060_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|CP034230.1_956056_956617_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|CP034230.1_956630_957689_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|CP034230.1_957699_958446_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|CP034230.1_958427_959078_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|CP034230.1_959074_959995_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|CP034230.1_959994_960288_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|CP034230.1_961874_962921_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|CP034230.1_963171_964080_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|CP034230.1_964089_965529_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|CP034230.1_965515_966121_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|119aa|down_4|CP034230.1_966138_966495_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|CP034230.1_966685_966997_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|CP034230.1_967015_967726_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|CP034230.1_967725_968205_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|CP034230.1_968201_969251_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|CP034230.1_969231_969993_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCA_003864015.1_ASM386401v1	CP034230	Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 14028 chromosome, complete genome	4	961283-961860	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,cas14j,RT	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAAC,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	27,29,29	0	0	NA	NA	I-E:I-E:I-E	9,9,9	9	TypeI-E	cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,cas14j,RT	NA|75aa|up_8|CP034230.1_951499_951724_-,NA	NA|318aa|up_9|CP034230.1_950430_951384_-	PRK15379, PRK15379, type III secretion system effector SopD	NA|75aa|up_8|CP034230.1_951499_951724_-	NA	cas3|888aa|up_7|CP034230.1_951828_954492_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|CP034230.1_954503_956060_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|CP034230.1_956056_956617_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|CP034230.1_956630_957689_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|CP034230.1_957699_958446_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|CP034230.1_958427_959078_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|CP034230.1_959074_959995_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|CP034230.1_959994_960288_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|CP034230.1_961874_962921_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|CP034230.1_963171_964080_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|CP034230.1_964089_965529_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|CP034230.1_965515_966121_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|119aa|down_4|CP034230.1_966138_966495_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|CP034230.1_966685_966997_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|CP034230.1_967015_967726_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|CP034230.1_967725_968205_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|CP034230.1_968201_969251_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|CP034230.1_969231_969993_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCA_003864015.1_ASM386401v1	CP034230	Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 14028 chromosome, complete genome	5	1152783-1152892	5	CRISPRCasFinder	no		cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,cas14j,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,cas14j,RT	NA,NA|276aa|down_2|CP034230.1_1155680_1156508_+,NA|198aa|down_4|CP034230.1_1158425_1159019_-	NA|212aa|up_9|CP034230.1_1144159_1144795_+	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase	NA|401aa|up_8|CP034230.1_1144868_1146071_-	pfam13020, DUF3883, Domain of unknown function (DUF3883)	NA|338aa|up_7|CP034230.1_1146365_1147379_-	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|327aa|up_6|CP034230.1_1147389_1148370_-	COG3732, SrlE, Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism]	NA|125aa|up_5|CP034230.1_1148366_1148741_-	COG3731, SrlB, Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]	NA|174aa|up_4|CP034230.1_1148737_1149259_-	COG3730, SrlA, Phosphotransferase system sorbitol-specific component IIC [Carbohydrate transport and metabolism]	NA|95aa|up_3|CP034230.1_1149371_1149656_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|119aa|up_2|CP034230.1_1149750_1150107_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|273aa|up_1|CP034230.1_1150260_1151079_-	pfam14491, DUF4435, Protein of unknown function (DUF4435)	NA|428aa|up_0|CP034230.1_1151123_1152407_-	COG3950, COG3950, Predicted ATP-binding protein involved in virulence [General function prediction only]	NA|690aa|down_0|CP034230.1_1152909_1154979_-	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|72aa|down_1|CP034230.1_1155014_1155230_-	COG3311, AlpA, Predicted transcriptional regulator [Transcription]	NA|276aa|down_2|CP034230.1_1155680_1156508_+	NA	NA|398aa|down_3|CP034230.1_1156842_1158036_-	pfam02810, SEC-C, SEC-C motif	NA|198aa|down_4|CP034230.1_1158425_1159019_-	NA	NA|56aa|down_5|CP034230.1_1159065_1159233_-	PRK09692, PRK09692, integrase; Provisional	NA|355aa|down_6|CP034230.1_1159246_1160311_-	PRK09692, PRK09692, integrase; Provisional	NA|388aa|down_7|CP034230.1_1160911_1162075_-	TIGR01843, Hemolysin_secretion_protein_D_plasmid, type I secretion membrane fusion protein, HlyD family	NA|727aa|down_8|CP034230.1_1162082_1164263_-	TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB family	NA|470aa|down_9|CP034230.1_1164259_1165669_-	TIGR01844, Proteases_secretion_protein_PrtF, type I secretion outer membrane protein, TolC family
