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_002224405.1_ASM222440v1	NZ_CP022450	Salmonella enterica subsp. enterica serovar Indiana strain D90 chromosome, complete genome	1	585138-585238	1	CRISPRCasFinder	no		cas3,PD-DExK,DEDDh,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DinG	Orphan	GCTTCAGTGGCGAGCGTCGTGAA	23	0	0	NA	NA	NA	1	1	Orphan	cas3,PD-DExK,DEDDh,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DinG	NA,NA|177aa|down_1|NZ_CP022450.1_586756_587287_-	NA|448aa|up_9|NZ_CP022450.1_571215_572559_-	PRK05370, PRK05370, argininosuccinate synthase; Validated	NA|151aa|up_8|NZ_CP022450.1_573186_573639_+	PRK00092, PRK00092, ribosome maturation protein RimP; Reviewed	NA|501aa|up_7|NZ_CP022450.1_573666_575169_+	PRK09202, nusA, transcription elongation factor NusA; Validated	NA|893aa|up_6|NZ_CP022450.1_575193_577872_+	PRK05306, infB, translation initiation factor IF-2; Validated	NA|134aa|up_5|NZ_CP022450.1_578093_578495_+	PRK00521, rbfA, 30S ribosome-binding factor RbfA	NA|315aa|up_4|NZ_CP022450.1_578494_579439_+	PRK05033, truB, tRNA pseudouridine synthase B; Provisional	NA|90aa|up_3|NZ_CP022450.1_579589_579859_+	PRK05626, rpsO, 30S ribosomal protein S15; Reviewed	NA|712aa|up_2|NZ_CP022450.1_580100_582236_+	PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase; Provisional	NA|295aa|up_1|NZ_CP022450.1_582345_583230_+	PRK11189, PRK11189, lipoprotein NlpI; Provisional	NA|27aa|up_0|NZ_CP022450.1_583335_583416_+	NF033440, small_YrbN, protein YrbN	NA|415aa|down_0|NZ_CP022450.1_585451_586696_+	PRK10483, PRK10483, tryptophan permease; Provisional	NA|177aa|down_1|NZ_CP022450.1_586756_587287_-	NA	NA|240aa|down_2|NZ_CP022450.1_587445_588165_+	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown]	NA|336aa|down_3|NZ_CP022450.1_588142_589150_-	PRK10508, PRK10508, luciferase-like monooxygenase	NA|299aa|down_4|NZ_CP022450.1_589327_590224_-	PRK15447, PRK15447, putative protease; Provisional	NA|332aa|down_5|NZ_CP022450.1_590214_591210_-	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|175aa|down_6|NZ_CP022450.1_591426_591951_+	COG3154, COG3154, Putative lipid carrier protein [Lipid metabolism]	NA|168aa|down_7|NZ_CP022450.1_591944_592448_+	COG3153, COG3153, Predicted acetyltransferase [General function prediction only]	NA|106aa|down_8|NZ_CP022450.1_592434_592752_-	PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated	NA|148aa|down_9|NZ_CP022450.1_592789_593233_+	PRK03467, PRK03467, hypothetical protein; Provisional
GCF_002224405.1_ASM222440v1	NZ_CP022450	Salmonella enterica subsp. enterica serovar Indiana strain D90 chromosome, complete genome	2	961066-962132	1,2,1	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	cas3,PD-DExK,DEDDh,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,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,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DinG	NA,NA	NA|179aa|up_9|NZ_CP022450.1_949609_950146_-	PRK15260, PRK15260, fimbrial protein SteF; Provisional	NA|157aa|up_8|NZ_CP022450.1_950142_950613_-	PRK15276, PRK15276, putative fimbrial subunit SteE; Provisional	NA|169aa|up_7|NZ_CP022450.1_950627_951134_-	PRK15275, PRK15275, putative fimbrial protein SteD; Provisional	NA|258aa|up_6|NZ_CP022450.1_951153_951927_-	PRK15274, PRK15274, putative periplasmic fimbrial chaperone protein SteC; Provisional	NA|900aa|up_5|NZ_CP022450.1_951939_954639_-	PRK15273, PRK15273, fimbrial biogenesis outer membrane usher protein	NA|196aa|up_4|NZ_CP022450.1_954718_955306_-	PRK15261, PRK15261, fimbrial protein SteA; Provisional	NA|267aa|up_3|NZ_CP022450.1_955915_956716_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_2|NZ_CP022450.1_956943_958581_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_1|NZ_CP022450.1_958663_959962_+	PRK00077, eno, enolase; Provisional	NA|224aa|up_0|NZ_CP022450.1_960097_960769_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|266aa|down_0|NZ_CP022450.1_962229_963027_+	COG1237, COG1237, Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]	NA|121aa|down_1|NZ_CP022450.1_963114_963477_-	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|600aa|down_2|NZ_CP022450.1_963900_965700_+	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|571aa|down_3|NZ_CP022450.1_965699_967412_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|down_4|NZ_CP022450.1_967487_968222_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|down_5|NZ_CP022450.1_968309_969263_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|900aa|down_6|NZ_CP022450.1_969643_972343_-	PRK09694, PRK09694, CRISPR-associated helicase/endonuclease Cas3	cas8e|512aa|down_7|NZ_CP022450.1_972700_974236_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|201aa|down_8|NZ_CP022450.1_974252_974855_+	TIGR02548, CRISPR_system_Cascade_subunit_CasB, CRISPR type I-E/ECOLI-associated protein CasB/Cse2	cas7|353aa|down_9|NZ_CP022450.1_974877_975936_+	pfam09344, Cas_CT1975, CT1975-like protein
GCF_002224405.1_ASM222440v1	NZ_CP022450	Salmonella enterica subsp. enterica serovar Indiana strain D90 chromosome, complete genome	3	978673-979738	2,3,2	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2	cas3,PD-DExK,DEDDh,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,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,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DinG	NA,NA	NA|245aa|up_9|NZ_CP022450.1_967487_968222_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|318aa|up_8|NZ_CP022450.1_968309_969263_-	PRK15379, PRK15379, type III secretion system effector SopD	cas3|900aa|up_7|NZ_CP022450.1_969643_972343_-	PRK09694, PRK09694, CRISPR-associated helicase/endonuclease Cas3	cas8e|512aa|up_6|NZ_CP022450.1_972700_974236_+	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cse2gr11|201aa|up_5|NZ_CP022450.1_974252_974855_+	TIGR02548, CRISPR_system_Cascade_subunit_CasB, CRISPR type I-E/ECOLI-associated protein CasB/Cse2	cas7|353aa|up_4|NZ_CP022450.1_974877_975936_+	pfam09344, Cas_CT1975, CT1975-like protein	cas5|242aa|up_3|NZ_CP022450.1_975945_976671_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|235aa|up_2|NZ_CP022450.1_976670_977375_+	cd09664, Cas6_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas6e	cas1|306aa|up_1|NZ_CP022450.1_977374_978292_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP022450.1_978294_978588_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|349aa|down_0|NZ_CP022450.1_979752_980799_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP022450.1_981049_981958_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|480aa|down_2|NZ_CP022450.1_981967_983407_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP022450.1_983393_983999_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP022450.1_984049_984373_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP022450.1_984563_984875_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP022450.1_984893_985604_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP022450.1_985603_986083_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP022450.1_986079_987129_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP022450.1_987109_987871_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_002224405.1_ASM222440v1	NZ_CP022450	Salmonella enterica subsp. enterica serovar Indiana strain D90 chromosome, complete genome	4	3615794-3615876	4	CRISPRCasFinder	no		cas3,PD-DExK,DEDDh,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DinG	Orphan	TGGACACTGGCTGGACATCGGCTGGACA	28	0	0	NA	NA	NA	1	1	Orphan	cas3,PD-DExK,DEDDh,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DinG	NA|146aa|up_6|NZ_CP022450.1_3611784_3612222_+,NA|67aa|up_4|NZ_CP022450.1_3612840_3613041_-,NA|66aa|up_2|NZ_CP022450.1_3613419_3613617_-,NA|49aa|down_0|NZ_CP022450.1_3616272_3616419_-,NA|78aa|down_2|NZ_CP022450.1_3617092_3617326_-,NA|114aa|down_4|NZ_CP022450.1_3618475_3618817_+,NA|92aa|down_5|NZ_CP022450.1_3619243_3619519_+,NA|90aa|down_6|NZ_CP022450.1_3619680_3619950_+,NA|53aa|down_7|NZ_CP022450.1_3619946_3620105_+	NA|204aa|up_9|NZ_CP022450.1_3610186_3610798_-	pfam05766, NinG, Bacteriophage Lambda NinG protein	NA|57aa|up_8|NZ_CP022450.1_3610790_3610961_-	PRK09689, PRK09689, prophage protein NinE; Provisional	NA|152aa|up_7|NZ_CP022450.1_3610960_3611416_-	PRK09741, PRK09741, hypothetical protein; Provisional	NA|146aa|up_6|NZ_CP022450.1_3611784_3612222_+	NA	NA|206aa|up_5|NZ_CP022450.1_3612223_3612841_-	pfam04448, DUF551, Protein of unknown function (DUF551)	NA|67aa|up_4|NZ_CP022450.1_3612840_3613041_-	NA	NA|130aa|up_3|NZ_CP022450.1_3613033_3613423_-	pfam13935, Ead_Ea22, Ead/Ea22-like protein	NA|66aa|up_2|NZ_CP022450.1_3613419_3613617_-	NA	NA|115aa|up_1|NZ_CP022450.1_3613613_3613958_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|478aa|up_0|NZ_CP022450.1_3613957_3615391_-	TIGR03600, phage_DnaB, phage replicative helicase, DnaB family, HK022 subfamily	NA|49aa|down_0|NZ_CP022450.1_3616272_3616419_-	NA	NA|189aa|down_1|NZ_CP022450.1_3616508_3617075_-	pfam06254, YdaT_toxin, Putative bacterial toxin ydaT	NA|78aa|down_2|NZ_CP022450.1_3617092_3617326_-	NA	NA|251aa|down_3|NZ_CP022450.1_3617367_3618120_+	COG1974, LexA, SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]	NA|114aa|down_4|NZ_CP022450.1_3618475_3618817_+	NA	NA|92aa|down_5|NZ_CP022450.1_3619243_3619519_+	NA	NA|90aa|down_6|NZ_CP022450.1_3619680_3619950_+	NA	NA|53aa|down_7|NZ_CP022450.1_3619946_3620105_+	NA	NA|70aa|down_8|NZ_CP022450.1_3620101_3620311_+	PRK11354, kil, FtsZ inhibitor protein; Reviewed	NA|324aa|down_9|NZ_CP022450.1_3620381_3621353_+	PTZ00121, PTZ00121, MAEBL; Provisional
GCF_002224405.1_ASM222440v1	NZ_CP022453	Salmonella enterica subsp. enterica serovar Indiana strain D90 plasmid pD90-3, complete sequence	1	5850-5969	1	CRISPRCasFinder	no	csa3	csa3	Type I-A	TGCGTACCCATCCACCTTTCAGTGCGTACCCATCCACCTTTCA	43	0	0	NA	NA	NA	1	1	Orphan	cas3,PD-DExK,DEDDh,WYL,cas8e,cse2gr11,cas7,cas5,cas6e,cas1,cas2,csa3,DinG	NA|118aa|up_3|NZ_CP022453.1_2954_3308_-,NA|149aa|up_2|NZ_CP022453.1_3444_3891_-,NA|63aa|down_3|NZ_CP022453.1_9059_9248_-	NA|NA	NA	NA|NA	NA	NA|NA	NA	NA|207aa|up_6|NZ_CP022453.1_26_647_+	cd02042, ParAB_family, partition proteins ParAB family	NA|77aa|up_5|NZ_CP022453.1_698_929_+	pfam09274, ParG, ParG	NA|355aa|up_4|NZ_CP022453.1_1352_2417_+	pfam13614, AAA_31, AAA domain	NA|118aa|up_3|NZ_CP022453.1_2954_3308_-	NA	NA|149aa|up_2|NZ_CP022453.1_3444_3891_-	NA	NA|281aa|up_1|NZ_CP022453.1_3894_4737_-	pfam01051, Rep_3, Initiator Replication protein	NA|280aa|up_0|NZ_CP022453.1_4757_5597_-	pfam01051, Rep_3, Initiator Replication protein	NA|84aa|down_0|NZ_CP022453.1_6831_7083_+	PRK02854, PRK02854, primosomal protein DnaT	NA|94aa|down_1|NZ_CP022453.1_7072_7354_+	COG2026, RelE, Cytotoxic translational repressor of toxin-antitoxin stability system [Translation, ribosomal structure and biogenesis / Cell division and chromosome partitioning]	NA|400aa|down_2|NZ_CP022453.1_7850_9050_-	pfam04986, Y2_Tnp, Putative transposase	NA|63aa|down_3|NZ_CP022453.1_9059_9248_-	NA	NA|265aa|down_4|NZ_CP022453.1_10826_11621_+	cd05150, APH, Aminoglycoside 3'-phosphotransferase	NA|235aa|down_5|NZ_CP022453.1_11927_12632_+	COG3316, COG3316, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|195aa|down_6|NZ_CP022453.1_13039_13624_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|235aa|down_7|NZ_CP022453.1_15889_16594_-	COG3316, COG3316, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|479aa|down_8|NZ_CP022453.1_16860_18297_+	pfam03917, GSH_synth_ATP, Eukaryotic glutathione synthase, ATP binding domain	NA|235aa|down_9|NZ_CP022453.1_19297_20002_-	pfam01051, Rep_3, Initiator Replication protein
