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_012053145.1_ASM1205314v1	NZ_CP050764	Salmonella enterica subsp. enterica serovar Indiana strain SI111 chromosome, complete genome	1	584882-584982	1	CRISPRCasFinder	no		cas3,PD-DExK,DEDDh,csa3,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DinG	Orphan	GCTTCAGTGGCGAGCGTCGTGAA	23	0	0	NA	NA	NA	1	1	Orphan	cas3,PD-DExK,DEDDh,csa3,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DinG	NA,NA|177aa|down_1|NZ_CP050764.1_586500_587031_-	NA|448aa|up_9|NZ_CP050764.1_570959_572303_-	PRK05370, PRK05370, argininosuccinate synthase; Validated	NA|151aa|up_8|NZ_CP050764.1_572930_573383_+	PRK00092, PRK00092, ribosome maturation protein RimP; Reviewed	NA|501aa|up_7|NZ_CP050764.1_573410_574913_+	PRK09202, nusA, transcription elongation factor NusA; Validated	NA|893aa|up_6|NZ_CP050764.1_574937_577616_+	PRK05306, infB, translation initiation factor IF-2; Validated	NA|134aa|up_5|NZ_CP050764.1_577837_578239_+	PRK00521, rbfA, 30S ribosome-binding factor RbfA	NA|315aa|up_4|NZ_CP050764.1_578238_579183_+	PRK05033, truB, tRNA pseudouridine synthase B; Provisional	NA|90aa|up_3|NZ_CP050764.1_579333_579603_+	PRK05626, rpsO, 30S ribosomal protein S15; Reviewed	NA|712aa|up_2|NZ_CP050764.1_579844_581980_+	PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional	NA|295aa|up_1|NZ_CP050764.1_582089_582974_+	PRK11189, PRK11189, lipoprotein NlpI; Provisional	NA|27aa|up_0|NZ_CP050764.1_583079_583160_+	NF033440, small_YrbN, protein YrbN	NA|415aa|down_0|NZ_CP050764.1_585195_586440_+	PRK10483, PRK10483, tryptophan permease; Provisional	NA|177aa|down_1|NZ_CP050764.1_586500_587031_-	NA	NA|240aa|down_2|NZ_CP050764.1_587189_587909_+	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown]	NA|336aa|down_3|NZ_CP050764.1_587886_588894_-	PRK10508, PRK10508, luciferase-like monooxygenase	NA|299aa|down_4|NZ_CP050764.1_589071_589968_-	PRK15447, PRK15447, putative protease; Provisional	NA|332aa|down_5|NZ_CP050764.1_589958_590954_-	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|175aa|down_6|NZ_CP050764.1_591170_591695_+	COG3154, COG3154, Putative lipid carrier protein [Lipid metabolism]	NA|168aa|down_7|NZ_CP050764.1_591688_592192_+	COG3153, COG3153, Predicted acetyltransferase [General function prediction only]	NA|106aa|down_8|NZ_CP050764.1_592178_592496_-	PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated	NA|148aa|down_9|NZ_CP050764.1_592533_592977_+	PRK03467, PRK03467, hypothetical protein; Provisional
GCF_012053145.1_ASM1205314v1	NZ_CP050764	Salmonella enterica subsp. enterica serovar Indiana strain SI111 chromosome, complete genome	2	796241-796360	2	CRISPRCasFinder	no		cas3,PD-DExK,DEDDh,csa3,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DinG	Orphan	TGCGTACCCATCCACCTTTCAGTGCGTACCCATCCACCTTTCA	43	0	0	NA	NA	NA	1	1	Orphan	cas3,PD-DExK,DEDDh,csa3,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DinG	NA|60aa|up_8|NZ_CP050764.1_789183_789363_+,NA|118aa|up_3|NZ_CP050764.1_793345_793699_-,NA|149aa|up_2|NZ_CP050764.1_793835_794282_-,NA|63aa|down_2|NZ_CP050764.1_799030_799219_-	NA|235aa|up_9|NZ_CP050764.1_786907_787612_-	COG3316, COG3316, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|60aa|up_8|NZ_CP050764.1_789183_789363_+	NA	NA|215aa|up_7|NZ_CP050764.1_789478_790123_-	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|207aa|up_6|NZ_CP050764.1_790417_791038_+	cd02042, ParAB_family, partition proteins ParAB family	NA|77aa|up_5|NZ_CP050764.1_791089_791320_+	pfam09274, ParG, ParG	NA|355aa|up_4|NZ_CP050764.1_791743_792808_+	pfam13614, AAA_31, AAA domain	NA|118aa|up_3|NZ_CP050764.1_793345_793699_-	NA	NA|149aa|up_2|NZ_CP050764.1_793835_794282_-	NA	NA|281aa|up_1|NZ_CP050764.1_794285_795128_-	pfam01051, Rep_3, Initiator Replication protein	NA|280aa|up_0|NZ_CP050764.1_795148_795988_-	pfam01051, Rep_3, Initiator Replication protein	NA|84aa|down_0|NZ_CP050764.1_797222_797474_+	PRK02854, PRK02854, primosomal protein DnaT	NA|400aa|down_1|NZ_CP050764.1_797821_799021_-	pfam04986, Y2_Tnp, Putative transposase	NA|63aa|down_2|NZ_CP050764.1_799030_799219_-	NA	NA|265aa|down_3|NZ_CP050764.1_800797_801592_+	cd05150, APH, Aminoglycoside 3'-phosphotransferase	NA|235aa|down_4|NZ_CP050764.1_801898_802603_+	COG3316, COG3316, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|186aa|down_5|NZ_CP050764.1_803134_803692_+	pfam11354, DUF3156, Protein of unknown function (DUF3156)	NA|228aa|down_6|NZ_CP050764.1_803796_804480_-	smart00421, HTH_LUXR, helix_turn_helix, Lux Regulon	NA|440aa|down_7|NZ_CP050764.1_806182_807502_-	COG4097, COG4097, Predicted ferric reductase [Inorganic ion transport and metabolism]	NA|88aa|down_8|NZ_CP050764.1_807577_807841_-	pfam07338, DUF1471, Protein of unknown function (DUF1471)	NA|305aa|down_9|NZ_CP050764.1_808590_809505_+	cd08422, PBP2_CrgA_like, The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain
GCF_012053145.1_ASM1205314v1	NZ_CP050764	Salmonella enterica subsp. enterica serovar Indiana strain SI111 chromosome, complete genome	3	992204-993270	1,3,1	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	cas3,PD-DExK,DEDDh,csa3,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	16,17,17	17	TypeI-E	cas3,PD-DExK,DEDDh,csa3,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DinG	NA,NA	NA|179aa|up_9|NZ_CP050764.1_980747_981284_-	PRK15260, PRK15260, fimbrial protein SteF; Provisional	NA|157aa|up_8|NZ_CP050764.1_981280_981751_-	PRK15276, PRK15276, putative fimbrial subunit SteE; Provisional	NA|169aa|up_7|NZ_CP050764.1_981765_982272_-	PRK15275, PRK15275, putative fimbrial protein SteD; Provisional	NA|258aa|up_6|NZ_CP050764.1_982291_983065_-	PRK15274, PRK15274, putative periplasmic fimbrial chaperone protein SteC; Provisional	NA|900aa|up_5|NZ_CP050764.1_983077_985777_-	PRK15273, PRK15273, fimbrial biogenesis outer membrane usher protein	NA|196aa|up_4|NZ_CP050764.1_985856_986444_-	PRK15261, PRK15261, fimbrial protein SteA; Provisional	NA|267aa|up_3|NZ_CP050764.1_987053_987854_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|NZ_CP050764.1_988081_989719_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|NZ_CP050764.1_989801_991100_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|NZ_CP050764.1_991235_991907_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|NZ_CP050764.1_993367_994165_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|NZ_CP050764.1_994252_994615_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|600aa|down_2|NZ_CP050764.1_995038_996838_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_3|NZ_CP050764.1_996837_998550_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_4|NZ_CP050764.1_998625_999360_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_5|NZ_CP050764.1_999447_1000401_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|900aa|down_6|NZ_CP050764.1_1000781_1003481_-	PRK09694, PRK09694, CRISPR-associated helicase/endonuclease Cas3	cas8e|512aa|down_7|NZ_CP050764.1_1003838_1005374_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|201aa|down_8|NZ_CP050764.1_1005390_1005993_+	TIGR02548, CRISPR_system_Cascade_subunit_CasB, CRISPR type I-E/ECOLI-associated protein CasB/Cse2	cas7|353aa|down_9|NZ_CP050764.1_1006015_1007074_+	pfam09344, Cas_CT1975, CT1975-like protein
GCF_012053145.1_ASM1205314v1	NZ_CP050764	Salmonella enterica subsp. enterica serovar Indiana strain SI111 chromosome, complete genome	4	1009811-1010876	2,4,2	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	cas3,PD-DExK,DEDDh,csa3,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DinG	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	17,17,17	17	TypeI-E	cas3,PD-DExK,DEDDh,csa3,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DinG	NA,NA	NA|245aa|up_9|NZ_CP050764.1_998625_999360_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP050764.1_999447_1000401_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|900aa|up_7|NZ_CP050764.1_1000781_1003481_-	PRK09694, PRK09694, CRISPR-associated helicase/endonuclease Cas3	cas8e|512aa|up_6|NZ_CP050764.1_1003838_1005374_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|201aa|up_5|NZ_CP050764.1_1005390_1005993_+	TIGR02548, CRISPR_system_Cascade_subunit_CasB, CRISPR type I-E/ECOLI-associated protein CasB/Cse2	cas7|353aa|up_4|NZ_CP050764.1_1006015_1007074_+	pfam09344, Cas_CT1975, CT1975-like protein	cas5|242aa|up_3|NZ_CP050764.1_1007083_1007809_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|235aa|up_2|NZ_CP050764.1_1007808_1008513_+	cd09664, Cas6_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas6e	cas1|306aa|up_1|NZ_CP050764.1_1008512_1009430_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP050764.1_1009432_1009726_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP050764.1_1010890_1011937_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP050764.1_1012187_1013096_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP050764.1_1013105_1014545_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP050764.1_1014531_1015137_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP050764.1_1015187_1015511_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP050764.1_1015701_1016013_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP050764.1_1016031_1016742_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP050764.1_1016741_1017221_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP050764.1_1017217_1018267_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP050764.1_1018247_1019009_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_012053145.1_ASM1205314v1	NZ_CP050765	Salmonella enterica subsp. enterica serovar Indiana strain SI111 plasmid pSI111-1, complete sequence	1	6550-6669	1	CRISPRCasFinder	no	csa3	csa3	Type I-A	TGAAAGGTGGATGGGTACGCACTGAAAGGTGGATGGGTACGCA	43	0	0	NA	NA	NA	1	1	Orphan	cas3,PD-DExK,DEDDh,csa3,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,DinG	NA|67aa|up_4|NZ_CP050765.1_1281_1482_-,NA|63aa|up_2|NZ_CP050765.1_3690_3879_+,NA|149aa|down_2|NZ_CP050765.1_8627_9074_+,NA|118aa|down_3|NZ_CP050765.1_9210_9564_+,NA|60aa|down_8|NZ_CP050765.1_13546_13726_-	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|63aa|up_5|NZ_CP050765.1_1045_1234_+	pfam01815, Rop, Rop protein	NA|67aa|up_4|NZ_CP050765.1_1281_1482_-	NA	NA|291aa|up_3|NZ_CP050765.1_2803_3676_+	pfam08376, NIT, Nitrate and nitrite sensing	NA|63aa|up_2|NZ_CP050765.1_3690_3879_+	NA	NA|400aa|up_1|NZ_CP050765.1_3888_5088_+	pfam04986, Y2_Tnp, Putative transposase	NA|84aa|up_0|NZ_CP050765.1_5435_5687_-	PRK02854, PRK02854, primosomal protein DnaT	NA|280aa|down_0|NZ_CP050765.1_6921_7761_+	pfam01051, Rep_3, Initiator Replication protein	NA|281aa|down_1|NZ_CP050765.1_7781_8624_+	pfam01051, Rep_3, Initiator Replication protein	NA|149aa|down_2|NZ_CP050765.1_8627_9074_+	NA	NA|118aa|down_3|NZ_CP050765.1_9210_9564_+	NA	NA|355aa|down_4|NZ_CP050765.1_10101_11166_-	pfam13614, AAA_31, AAA domain	NA|77aa|down_5|NZ_CP050765.1_11589_11820_-	pfam09274, ParG, ParG	NA|207aa|down_6|NZ_CP050765.1_11871_12492_-	cd02042, ParAB_family, partition proteins ParAB family	NA|215aa|down_7|NZ_CP050765.1_12786_13431_+	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|down_8|NZ_CP050765.1_13546_13726_-	NA	NA|235aa|down_9|NZ_CP050765.1_15297_16002_+	COG3316, COG3316, Transposase and inactivated derivatives [DNA replication, recombination, and repair]
