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_012049605.1_ASM1204960v1	NZ_CP050745	Salmonella enterica subsp. enterica serovar Typhimurium strain ST53 chromosome, complete genome	1	678225-678325	1	CRISPRCasFinder	no		csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,DEDDh,DinG,RT	Orphan	GCTTCAGTGGCGAACGTCGTGAA	23	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,DEDDh,DinG,RT	NA,NA|177aa|down_1|NZ_CP050745.1_679843_680374_-	NA|448aa|up_9|NZ_CP050745.1_664303_665647_-	PRK05370, PRK05370, argininosuccinate synthase; Validated	NA|151aa|up_8|NZ_CP050745.1_666274_666727_+	PRK00092, PRK00092, ribosome maturation protein RimP; Reviewed	NA|501aa|up_7|NZ_CP050745.1_666754_668257_+	PRK09202, nusA, transcription elongation factor NusA; Validated	NA|893aa|up_6|NZ_CP050745.1_668281_670960_+	PRK05306, infB, translation initiation factor IF-2; Validated	NA|134aa|up_5|NZ_CP050745.1_671180_671582_+	PRK00521, rbfA, 30S ribosome-binding factor RbfA	NA|315aa|up_4|NZ_CP050745.1_671581_672526_+	PRK05033, truB, tRNA pseudouridine synthase B; Provisional	NA|90aa|up_3|NZ_CP050745.1_672676_672946_+	PRK05626, rpsO, 30S ribosomal protein S15; Reviewed	NA|712aa|up_2|NZ_CP050745.1_673187_675323_+	PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional	NA|295aa|up_1|NZ_CP050745.1_675432_676317_+	PRK11189, PRK11189, lipoprotein NlpI; Provisional	NA|27aa|up_0|NZ_CP050745.1_676422_676503_+	NF033440, small_YrbN, protein YrbN	NA|415aa|down_0|NZ_CP050745.1_678538_679783_+	PRK10483, PRK10483, tryptophan permease; Provisional	NA|177aa|down_1|NZ_CP050745.1_679843_680374_-	NA	NA|240aa|down_2|NZ_CP050745.1_680532_681252_+	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown]	NA|336aa|down_3|NZ_CP050745.1_681229_682237_-	PRK10508, PRK10508, luciferase-like monooxygenase	NA|299aa|down_4|NZ_CP050745.1_682414_683311_-	PRK15447, PRK15447, putative protease; Provisional	NA|332aa|down_5|NZ_CP050745.1_683301_684297_-	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|175aa|down_6|NZ_CP050745.1_684513_685038_+	COG3154, COG3154, Putative lipid carrier protein [Lipid metabolism]	NA|168aa|down_7|NZ_CP050745.1_685031_685535_+	COG3153, COG3153, Predicted acetyltransferase [General function prediction only]	NA|106aa|down_8|NZ_CP050745.1_685521_685839_-	PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated	NA|148aa|down_9|NZ_CP050745.1_685876_686320_+	PRK03467, PRK03467, hypothetical protein; Provisional
GCF_012049605.1_ASM1204960v1	NZ_CP050745	Salmonella enterica subsp. enterica serovar Typhimurium strain ST53 chromosome, complete genome	2	1028172-1030153	1,2,1	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,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	csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,DEDDh,DinG,RT	NA,NA	NA|381aa|up_9|NZ_CP050745.1_1013970_1015113_+	COG1929, COG1929, Glycerate kinase [Carbohydrate transport and metabolism]	NA|919aa|up_8|NZ_CP050745.1_1015156_1017913_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|432aa|up_7|NZ_CP050745.1_1017970_1019266_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_6|NZ_CP050745.1_1019317_1021552_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|119aa|up_5|NZ_CP050745.1_1021635_1021992_+	COG3609, COG3609, Predicted transcriptional regulators containing the CopG/Arc/MetJ DNA-binding domain [Transcription]	NA|99aa|up_4|NZ_CP050745.1_1021957_1022254_+	COG3668, ParE, Plasmid stabilization system protein [General function prediction only]	NA|267aa|up_3|NZ_CP050745.1_1023021_1023822_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|NZ_CP050745.1_1024049_1025687_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|NZ_CP050745.1_1025769_1027068_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|NZ_CP050745.1_1027203_1027875_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|NZ_CP050745.1_1030250_1031048_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|NZ_CP050745.1_1031135_1031498_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|600aa|down_2|NZ_CP050745.1_1031921_1033721_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_3|NZ_CP050745.1_1033720_1035433_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_4|NZ_CP050745.1_1035508_1036243_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_5|NZ_CP050745.1_1036330_1037284_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|down_6|NZ_CP050745.1_1037728_1040392_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|down_7|NZ_CP050745.1_1040403_1041960_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|down_8|NZ_CP050745.1_1041956_1042517_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|down_9|NZ_CP050745.1_1042530_1043589_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI
GCF_012049605.1_ASM1204960v1	NZ_CP050745	Salmonella enterica subsp. enterica serovar Typhimurium strain ST53 chromosome, complete genome	3	1046285-1047169	2,3,2,3	PILER-CR,CRISPRCasFinder,CRT,PILER-CR	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,DEDDh,DinG,RT	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACC	29,29,29,28	0	0	NA	NA	I-E:I-E:I-E:I-E	11,14,14,11	14	TypeI-E	csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,DEDDh,DinG,RT	NA,NA	NA|245aa|up_9|NZ_CP050745.1_1035508_1036243_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP050745.1_1036330_1037284_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP050745.1_1037728_1040392_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP050745.1_1040403_1041960_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP050745.1_1041956_1042517_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP050745.1_1042530_1043589_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP050745.1_1043599_1044346_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP050745.1_1044327_1044978_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP050745.1_1044974_1045895_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP050745.1_1045894_1046188_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP050745.1_1047651_1048698_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP050745.1_1048948_1049857_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP050745.1_1049866_1051306_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP050745.1_1051292_1051898_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP050745.1_1051948_1052272_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP050745.1_1052462_1052774_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP050745.1_1052792_1053503_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP050745.1_1053502_1053982_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP050745.1_1053978_1055028_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP050745.1_1055008_1055770_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_012049605.1_ASM1204960v1	NZ_CP050745	Salmonella enterica subsp. enterica serovar Typhimurium strain ST53 chromosome, complete genome	4	1047243-1047637	4,4,3	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,DEDDh,DinG,RT	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	5,6,6	6	TypeI-E	csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,DEDDh,DinG,RT	NA,NA	NA|245aa|up_9|NZ_CP050745.1_1035508_1036243_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP050745.1_1036330_1037284_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|888aa|up_7|NZ_CP050745.1_1037728_1040392_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas8e|519aa|up_6|NZ_CP050745.1_1040403_1041960_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|187aa|up_5|NZ_CP050745.1_1041956_1042517_+	cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2	cas7|353aa|up_4|NZ_CP050745.1_1042530_1043589_+	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cas5|249aa|up_3|NZ_CP050745.1_1043599_1044346_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP050745.1_1044327_1044978_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP050745.1_1044974_1045895_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP050745.1_1045894_1046188_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP050745.1_1047651_1048698_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP050745.1_1048948_1049857_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP050745.1_1049866_1051306_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP050745.1_1051292_1051898_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP050745.1_1051948_1052272_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP050745.1_1052462_1052774_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP050745.1_1052792_1053503_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP050745.1_1053502_1053982_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP050745.1_1053978_1055028_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP050745.1_1055008_1055770_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_012049605.1_ASM1204960v1	NZ_CP050745	Salmonella enterica subsp. enterica serovar Typhimurium strain ST53 chromosome, complete genome	5	1386604-1386713	5	CRISPRCasFinder	no		csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,DEDDh,DinG,RT	Orphan	TTAAAAAAAGGTGGTACAGGGTGGGACA	28	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,DEDDh,DinG,RT	NA|80aa|up_7|NZ_CP050745.1_1376838_1377078_-,NA|198aa|up_4|NZ_CP050745.1_1380476_1381070_+,NA|276aa|up_2|NZ_CP050745.1_1382987_1383815_-,NA	NA|78aa|up_9|NZ_CP050745.1_1376052_1376286_-	pfam10893, DUF2724, Protein of unknown function (DUF2724)	NA|170aa|up_8|NZ_CP050745.1_1376293_1376803_-	pfam06892, Phage_CP76, Phage regulatory protein CII (CP76)	NA|80aa|up_7|NZ_CP050745.1_1376838_1377078_-	NA	NA|211aa|up_6|NZ_CP050745.1_1377194_1377827_+	pfam16452, Phage_CI_C, Bacteriophage CI repressor C-terminal domain	NA|342aa|up_5|NZ_CP050745.1_1377830_1378856_+	PHA02601, int, integrase; Provisional	NA|198aa|up_4|NZ_CP050745.1_1380476_1381070_+	NA	NA|398aa|up_3|NZ_CP050745.1_1381459_1382653_+	pfam02810, SEC-C, SEC-C motif	NA|276aa|up_2|NZ_CP050745.1_1382987_1383815_-	NA	NA|72aa|up_1|NZ_CP050745.1_1384265_1384481_+	COG3311, AlpA, Predicted transcriptional regulator [Transcription]	NA|690aa|up_0|NZ_CP050745.1_1384516_1386586_+	COG5519, COG5519, Superfamily II helicase and inactivated derivatives [DNA replication, recombination, and repair]	NA|428aa|down_0|NZ_CP050745.1_1387088_1388372_+	COG3950, COG3950, Predicted ATP-binding protein involved in virulence [General function prediction only]	NA|273aa|down_1|NZ_CP050745.1_1388416_1389235_+	pfam14491, DUF4435, Protein of unknown function (DUF4435)	NA|119aa|down_2|NZ_CP050745.1_1389388_1389745_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|95aa|down_3|NZ_CP050745.1_1389839_1390124_+	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|174aa|down_4|NZ_CP050745.1_1390236_1390758_+	COG3730, SrlA, Phosphotransferase system sorbitol-specific component IIC [Carbohydrate transport and metabolism]	NA|125aa|down_5|NZ_CP050745.1_1390754_1391129_+	COG3731, SrlB, Phosphotransferase system sorbitol-specific component IIA [Carbohydrate transport and metabolism]	NA|327aa|down_6|NZ_CP050745.1_1391125_1392106_+	COG3732, SrlE, Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism]	NA|338aa|down_7|NZ_CP050745.1_1392116_1393130_+	COG0673, MviM, Predicted dehydrogenases and related proteins [General function prediction only]	NA|401aa|down_8|NZ_CP050745.1_1393424_1394627_+	pfam13020, DUF3883, Domain of unknown function (DUF3883)	NA|212aa|down_9|NZ_CP050745.1_1394700_1395336_-	TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase
GCF_012049605.1_ASM1204960v1	NZ_CP050748	Salmonella enterica subsp. enterica serovar Typhimurium strain ST53 plasmid pST53-3, complete sequence	1	5835-5954	1	CRISPRCasFinder	no			Orphan	TGAAAGGTGGATGGGTACGCACTGAAAGGTGGATGGGTACGCA	43	0	0	NA	NA	NA	1	1	Orphan	csa3,cas3,PD-DExK,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,cas14j,DEDDh,DinG,RT	NA|60aa|up_2|NZ_CP050748.1_1585_1765_-,NA|63aa|up_0|NZ_CP050748.1_4916_5105_-,NA|149aa|down_2|NZ_CP050748.1_7912_8359_+,NA|118aa|down_3|NZ_CP050748.1_8495_8849_+	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|215aa|up_3|NZ_CP050748.1_825_1470_+	cd03767, SR_Res_par, Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme	NA|60aa|up_2|NZ_CP050748.1_1585_1765_-	NA	NA|235aa|up_1|NZ_CP050748.1_3336_4041_+	COG3316, COG3316, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|63aa|up_0|NZ_CP050748.1_4916_5105_-	NA	NA|280aa|down_0|NZ_CP050748.1_6206_7046_+	pfam01051, Rep_3, Initiator Replication protein	NA|281aa|down_1|NZ_CP050748.1_7066_7909_+	pfam01051, Rep_3, Initiator Replication protein	NA|149aa|down_2|NZ_CP050748.1_7912_8359_+	NA	NA|118aa|down_3|NZ_CP050748.1_8495_8849_+	NA	NA|355aa|down_4|NZ_CP050748.1_9386_10451_-	pfam13614, AAA_31, AAA domain	NA|77aa|down_5|NZ_CP050748.1_10874_11105_-	pfam09274, ParG, ParG	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA
