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_009912495.1_ASM991249v1	NZ_CP047785	Staphylococcus aureus strain UP_1186 chromosome, complete genome	1	395650-395730	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	AATTTCAACAGGCAATGCAAGTTGG	25	1	4	395675-395705|395675-395705|395675-395705|395675-395705	NZ_CP047785.1_1769686-1769656|NZ_CP047785.1_2668817-2668787|NZ_CP047785.1_1769574-1769544|NZ_CP047785.1_1769630-1769600	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|43aa|up_8|NZ_CP047785.1_388350_388479_+,NA|49aa|up_3|NZ_CP047785.1_391515_391662_+,NA	NA|589aa|up_9|NZ_CP047785.1_386252_388019_+	PRK00476, aspS, aspartyl-tRNA synthetase; Validated	NA|43aa|up_8|NZ_CP047785.1_388350_388479_+	NA	NA|258aa|up_7|NZ_CP047785.1_388478_389252_+	COG1179, COG1179, Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]	NA|425aa|up_6|NZ_CP047785.1_389412_390687_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|141aa|up_5|NZ_CP047785.1_390771_391194_+	COG1959, COG1959, Predicted transcriptional regulator [Transcription]	NA|61aa|up_4|NZ_CP047785.1_391293_391476_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|49aa|up_3|NZ_CP047785.1_391515_391662_+	NA	NA|338aa|up_2|NZ_CP047785.1_391898_392912_-	TIGR03558, oxido_grp_1, luciferase family oxidoreductase, group 1	NA|381aa|up_1|NZ_CP047785.1_393223_394366_+	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]	NA|373aa|up_0|NZ_CP047785.1_394366_395485_+	PRK00143, mnmA, tRNA-specific 2-thiouridylase MnmA; Reviewed	NA|223aa|down_0|NZ_CP047785.1_396001_396670_+	sd00006, TPR, Tetratricopeptide repeat	NA|826aa|down_1|NZ_CP047785.1_396671_399149_+	TIGR01448, recD_rel, helicase, putative, RecD/TraA family	NA|877aa|down_2|NZ_CP047785.1_399491_402122_+	PRK00252, alaS, alanyl-tRNA synthetase; Reviewed	NA|87aa|down_3|NZ_CP047785.1_402184_402445_+	PRK05473, IreB-like, IreB family regulatory phosphoprotein	NA|143aa|down_4|NZ_CP047785.1_402448_402877_+	COG0816, COG0816, Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasmas and B	NA|103aa|down_5|NZ_CP047785.1_402891_403200_+	PRK13678, PRK13678, hypothetical protein; Provisional	NA|213aa|down_6|NZ_CP047785.1_403484_404123_+	COG4122, COG4122, Predicted O-methyltransferase [General function prediction only]	NA|308aa|down_7|NZ_CP047785.1_404125_405049_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|423aa|down_8|NZ_CP047785.1_405060_406329_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|208aa|down_9|NZ_CP047785.1_406328_406952_+	PRK05480, PRK05480, uridine/cytidine kinase; Provisional
GCF_009912495.1_ASM991249v1	NZ_CP047785	Staphylococcus aureus strain UP_1186 chromosome, complete genome	2	1124120-1124205	2	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CCAACTTGCACATTATTGTAAGCTGGCTTT	30	1	3	1124150-1124175|1124150-1124175|1124150-1124175	NZ_CP047785.1_1211447-1211422|NZ_CP047785.1_1806926-1806951|NZ_CP047785.1_2471515-2471540	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA	NA|301aa|up_9|NZ_CP047785.1_1107556_1108459_-	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]	NA|1218aa|up_8|NZ_CP047785.1_1108624_1112278_-	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|1159aa|up_7|NZ_CP047785.1_1112278_1115755_-	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|192aa|up_6|NZ_CP047785.1_1115914_1116490_-	TIGR02227, Inactive_signal_peptidase_IA	NA|175aa|up_5|NZ_CP047785.1_1116505_1117030_-	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|up_4|NZ_CP047785.1_1117034_1117610_-	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|444aa|up_3|NZ_CP047785.1_1118535_1119867_-	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional	NA|402aa|up_2|NZ_CP047785.1_1120217_1121423_+	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|460aa|up_1|NZ_CP047785.1_1121412_1122792_+	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|310aa|up_0|NZ_CP047785.1_1123033_1123963_+	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins	NA|415aa|down_0|NZ_CP047785.1_1124411_1125656_-	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_1|NZ_CP047785.1_1125764_1126955_-	PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional	NA|376aa|down_2|NZ_CP047785.1_1127262_1128390_-	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|126aa|down_3|NZ_CP047785.1_1128750_1129128_-	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	NA|198aa|down_4|NZ_CP047785.1_1129543_1130137_-	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain	NA|128aa|down_5|NZ_CP047785.1_1130200_1130584_+	pfam08810, KapB, Kinase associated protein B	NA|802aa|down_6|NZ_CP047785.1_1130714_1133120_+	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed	NA|143aa|down_7|NZ_CP047785.1_1133112_1133541_+	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B	NA|110aa|down_8|NZ_CP047785.1_1133552_1133882_+	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed	NA|499aa|down_9|NZ_CP047785.1_1133874_1135371_+	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed
GCF_009912495.1_ASM991249v1	NZ_CP047785	Staphylococcus aureus strain UP_1186 chromosome, complete genome	3	2270000-2270133	1	PILER-CR	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	TATTGAAGAAGATACAA	17	1	1	2270080-2270116	NZ_CP047785.1_2266510-2266546	NA	2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|103aa|down_1|NZ_CP047785.1_2271766_2272075_-,NA|89aa|down_2|NZ_CP047785.1_2272214_2272481_-,NA|109aa|down_8|NZ_CP047785.1_2282261_2282588_+,NA|96aa|down_9|NZ_CP047785.1_2282590_2282878_+	NA|204aa|up_9|NZ_CP047785.1_2252125_2252737_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|426aa|up_8|NZ_CP047785.1_2253283_2254561_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_7|NZ_CP047785.1_2255472_2257296_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_6|NZ_CP047785.1_2257434_2257851_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_5|NZ_CP047785.1_2258081_2258774_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|255aa|up_4|NZ_CP047785.1_2258938_2259703_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_3|NZ_CP047785.1_2259856_2260537_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_2|NZ_CP047785.1_2260560_2262114_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_1|NZ_CP047785.1_2262230_2263589_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|978aa|up_0|NZ_CP047785.1_2264057_2266991_+	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|289aa|down_0|NZ_CP047785.1_2270773_2271640_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|103aa|down_1|NZ_CP047785.1_2271766_2272075_-	NA	NA|89aa|down_2|NZ_CP047785.1_2272214_2272481_-	NA	NA|603aa|down_3|NZ_CP047785.1_2272764_2274573_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_4|NZ_CP047785.1_2274704_2275097_+	cd03425, MutT_pyrophosphohydrolase, The MutT pyrophosphohydrolase is a prototypical Nudix hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic pyrophosphate (PPi)	NA|954aa|down_5|NZ_CP047785.1_2275098_2277960_+	COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	NA|253aa|down_6|NZ_CP047785.1_2278265_2279024_+	pfam04507, DUF576, Csa1 family	NA|258aa|down_7|NZ_CP047785.1_2279135_2279909_+	pfam04507, DUF576, Csa1 family	NA|109aa|down_8|NZ_CP047785.1_2282261_2282588_+	NA	NA|96aa|down_9|NZ_CP047785.1_2282590_2282878_+	NA
GCF_009912495.1_ASM991249v1	NZ_CP047785	Staphylococcus aureus strain UP_1186 chromosome, complete genome	4	2353746-2353839	3	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	CCTTTCTAACAAATAAATTTGAAGAA	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|35aa|up_0|NZ_CP047785.1_2353446_2353551_+,NA|35aa|down_2|NZ_CP047785.1_2356012_2356117_-	NA|453aa|up_9|NZ_CP047785.1_2343379_2344738_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|up_8|NZ_CP047785.1_2344739_2345747_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|up_7|NZ_CP047785.1_2345724_2346840_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|up_6|NZ_CP047785.1_2346850_2347543_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|up_5|NZ_CP047785.1_2347553_2348021_+	pfam06177, QueT, QueT transporter	NA|326aa|up_4|NZ_CP047785.1_2348079_2349057_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|316aa|up_3|NZ_CP047785.1_2349058_2350006_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|310aa|up_2|NZ_CP047785.1_2350573_2351503_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|438aa|up_1|NZ_CP047785.1_2352038_2353352_-	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|35aa|up_0|NZ_CP047785.1_2353446_2353551_+	NA	NA|289aa|down_0|NZ_CP047785.1_2353979_2354846_+	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|229aa|down_1|NZ_CP047785.1_2355172_2355859_+	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|35aa|down_2|NZ_CP047785.1_2356012_2356117_-	NA	NA|260aa|down_3|NZ_CP047785.1_2357840_2358620_+	cd13711, PBP2_Ngo0372_TcyA, Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold	NA|240aa|down_4|NZ_CP047785.1_2358600_2359320_+	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|244aa|down_5|NZ_CP047785.1_2359316_2360048_+	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|417aa|down_6|NZ_CP047785.1_2360144_2361395_-	pfam02388, FemAB, FemAB family	NA|121aa|down_7|NZ_CP047785.1_2361649_2362012_+	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|200aa|down_8|NZ_CP047785.1_2362030_2362630_+	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]	NA|516aa|down_9|NZ_CP047785.1_2362921_2364469_+	pfam09223, ZinT, ZinT (YodA) periplasmic lipocalin-like zinc-recruitment
GCF_009912495.1_ASM991249v1	NZ_CP047785	Staphylococcus aureus strain UP_1186 chromosome, complete genome	5	2544664-2544796	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL	Orphan	GAAACCAATGATATCAAGGGTTTTGTGAGCTTTCGAGTAAAGAG	44	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA,NA|61aa|down_0|NZ_CP047785.1_2545706_2545889_+,NA|67aa|down_1|NZ_CP047785.1_2545870_2546071_-,NA|93aa|down_7|NZ_CP047785.1_2552426_2552705_-	NA|130aa|up_9|NZ_CP047785.1_2536139_2536529_+	PRK05309, PRK05309, 30S ribosomal protein S11; Validated	NA|315aa|up_8|NZ_CP047785.1_2536603_2537548_+	PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional	NA|123aa|up_7|NZ_CP047785.1_2537564_2537933_+	PRK05591, rplQ, 50S ribosomal protein L17; Validated	NA|270aa|up_6|NZ_CP047785.1_2538470_2539280_+	PRK13648, cbiO, cobalt transporter ATP-binding subunit; Provisional	NA|287aa|up_5|NZ_CP047785.1_2539276_2540137_+	PRK13646, cbiO, energy-coupling factor transporter ATPase	NA|269aa|up_4|NZ_CP047785.1_2540126_2540933_+	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|268aa|up_3|NZ_CP047785.1_2540937_2541741_+	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|146aa|up_2|NZ_CP047785.1_2541980_2542418_+	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|133aa|up_1|NZ_CP047785.1_2542431_2542830_+	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|479aa|up_0|NZ_CP047785.1_2543178_2544615_+	COG2865, COG2865, Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]	NA|61aa|down_0|NZ_CP047785.1_2545706_2545889_+	NA	NA|67aa|down_1|NZ_CP047785.1_2545870_2546071_-	NA	NA|555aa|down_2|NZ_CP047785.1_2546359_2548024_+	PRK08617, PRK08617, acetolactate synthase AlsS	NA|235aa|down_3|NZ_CP047785.1_2548060_2548765_+	COG3527, AlsD, Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]	NA|142aa|down_4|NZ_CP047785.1_2549140_2549566_-	pfam03642, MAP, MAP domain	NA|272aa|down_5|NZ_CP047785.1_2549859_2550675_+	cd02605, HAD_SPP, sucrose-phosphatase, similar to Synechocystis sp PCC 6803 SPP	NA|506aa|down_6|NZ_CP047785.1_2550899_2552417_-	cd04949, GT4_GtfA-like, accessory Sec system glycosyltransferase GtfA and similar proteins	NA|93aa|down_7|NZ_CP047785.1_2552426_2552705_-	NA	NA|285aa|down_8|NZ_CP047785.1_2553579_2554434_+	COG0739, NlpD, Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]	NA|807aa|down_9|NZ_CP047785.1_2554632_2557053_-	cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase family
GCF_009912495.1_ASM991249v1	NZ_CP047785	Staphylococcus aureus strain UP_1186 chromosome, complete genome	6	2624206-2624294	5	CRISPRCasFinder	no	csa3	DEDDh,csa3,cas3,DinG,WYL	Type I-A	TGCATAAGAGCCCCTAACAACTAAAGTTTAAG	32	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL	NA|31aa|up_0|NZ_CP047785.1_2623993_2624086_-,NA|364aa|down_0|NZ_CP047785.1_2624307_2625399_-,NA|77aa|down_5|NZ_CP047785.1_2629185_2629416_+	NA|452aa|up_9|NZ_CP047785.1_2604870_2606226_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|2440aa|up_8|NZ_CP047785.1_2606509_2613829_+	TIGR04263, cell_wall_surface_anchor_family_protein, SasC/Mrp/FmtB intercellular aggregation domain	NA|369aa|up_7|NZ_CP047785.1_2614151_2615258_-	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|145aa|up_6|NZ_CP047785.1_2615257_2615692_-	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|711aa|up_5|NZ_CP047785.1_2615703_2617836_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|517aa|up_4|NZ_CP047785.1_2617870_2619421_-	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|602aa|up_3|NZ_CP047785.1_2620101_2621907_+	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|261aa|up_2|NZ_CP047785.1_2622139_2622922_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|up_1|NZ_CP047785.1_2622989_2623847_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|31aa|up_0|NZ_CP047785.1_2623993_2624086_-	NA	NA|364aa|down_0|NZ_CP047785.1_2624307_2625399_-	NA	NA|326aa|down_1|NZ_CP047785.1_2625664_2626642_-	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	csa3|107aa|down_2|NZ_CP047785.1_2626643_2626964_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|222aa|down_3|NZ_CP047785.1_2627115_2627781_+	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	NA|313aa|down_4|NZ_CP047785.1_2628216_2629155_+	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|77aa|down_5|NZ_CP047785.1_2629185_2629416_+	NA	NA|458aa|down_6|NZ_CP047785.1_2630089_2631463_+	pfam01878, EVE, EVE domain	NA|138aa|down_7|NZ_CP047785.1_2631920_2632334_+	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|148aa|down_8|NZ_CP047785.1_2632533_2632977_+	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|237aa|down_9|NZ_CP047785.1_2633097_2633808_-	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase
