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_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	1	34009-34102	1	CRISPRCasFinder	no	csa3	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Type I-A	GCAATGCGCGTTGGGGTGTGGGGCCCCAACATAG	34	1	1	34043-34068	NZ_LT992472.1_131831-131806	NA	1	1	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA|75aa|up_5|NZ_LT992472.1_30102_30327_-,NA|148aa|up_2|NZ_LT992472.1_31538_31982_-,NA|101aa|down_1|NZ_LT992472.1_35236_35539_+	NA|501aa|up_9|NZ_LT992472.1_25126_26629_-	COG4529, COG4529, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|105aa|up_8|NZ_LT992472.1_27279_27594_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|431aa|up_7|NZ_LT992472.1_27593_28886_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|285aa|up_6|NZ_LT992472.1_28972_29827_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|75aa|up_5|NZ_LT992472.1_30102_30327_-	NA	NA|157aa|up_4|NZ_LT992472.1_30525_30996_+	COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]	NA|148aa|up_3|NZ_LT992472.1_31108_31552_+	pfam06338, ComK, ComK protein	NA|148aa|up_2|NZ_LT992472.1_31538_31982_-	NA	NA|212aa|up_1|NZ_LT992472.1_32279_32915_+	pfam02517, Abi, CAAX protease self-immunity	NA|207aa|up_0|NZ_LT992472.1_33081_33702_+	pfam02517, Abi, CAAX protease self-immunity	NA|238aa|down_0|NZ_LT992472.1_34264_34978_-	PRK12376, PRK12376, putative translaldolase; Provisional	NA|101aa|down_1|NZ_LT992472.1_35236_35539_+	NA	NA|122aa|down_2|NZ_LT992472.1_35793_36159_+	PRK14201, PRK14201, fluoride efflux transporter CrcB	NA|118aa|down_3|NZ_LT992472.1_36155_36509_+	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|278aa|down_4|NZ_LT992472.1_36758_37592_-	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]	NA|303aa|down_5|NZ_LT992472.1_37803_38712_-	pfam08378, NERD, Nuclease-related domain	NA|398aa|down_6|NZ_LT992472.1_38836_40030_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|531aa|down_7|NZ_LT992472.1_40401_41994_+	cd00484, PEPCK_ATP, Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis	NA|249aa|down_8|NZ_LT992472.1_42290_43037_-	COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]	NA|158aa|down_9|NZ_LT992472.1_43041_43515_-	TIGR02705, conserved_hypothetical_protein, nucleoside triphosphatase YtkD
GCF_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	2	274872-275084	2	CRISPRCasFinder	no		csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Orphan	TGATGTGCTGTTGTGGAAGCTTGGTGTCGTGCCATGCTACTTTGATG	47	0	0	NA	NA	NA	2	2	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA|46aa|up_4|NZ_LT992472.1_271733_271871_-,NA|107aa|down_0|NZ_LT992472.1_275117_275438_+	NA|232aa|up_9|NZ_LT992472.1_264425_265121_+	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|507aa|up_8|NZ_LT992472.1_265473_266994_-	COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	NA|452aa|up_7|NZ_LT992472.1_267509_268865_-	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	NA|357aa|up_6|NZ_LT992472.1_268879_269950_-	PRK01966, ddl, D-alanine--D-alanine ligase	NA|401aa|up_5|NZ_LT992472.1_270267_271470_+	TIGR02210, Rod_shape-determining_protein_RodA, rod shape-determining protein RodA	NA|46aa|up_4|NZ_LT992472.1_271733_271871_-	NA	NA|70aa|up_3|NZ_LT992472.1_271998_272208_-	cd00371, HMA, Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones	NA|98aa|up_2|NZ_LT992472.1_272219_272513_-	cd10152, SaCsoR-like_DUF156, Staphylococcus aureus copper-sensitive operon repressor (CsoR), and related domains; this family was previously known as part of DUF156	NA|495aa|up_1|NZ_LT992472.1_272678_274163_+	TIGR04265, bac_cardiolipin, cardiolipin synthase	NA|216aa|up_0|NZ_LT992472.1_274190_274838_+	COG1418, COG1418, Predicted HD superfamily hydrolase [General function prediction only]	NA|107aa|down_0|NZ_LT992472.1_275117_275438_+	NA	NA|291aa|down_1|NZ_LT992472.1_277079_277952_-	PRK02463, PRK02463, OxaA-like protein precursor; Provisional	NA|214aa|down_2|NZ_LT992472.1_278037_278679_-	PRK00043, thiE, thiamine phosphate synthase	NA|264aa|down_3|NZ_LT992472.1_278680_279472_-	PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated	NA|277aa|down_4|NZ_LT992472.1_279455_280286_-	PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed	NA|230aa|down_5|NZ_LT992472.1_280278_280968_-	TIGR04306, salvage_TenA, thiaminase II	NA|232aa|down_6|NZ_LT992472.1_281354_282050_-	pfam06737, Transglycosylas, Transglycosylase-like domain	NA|132aa|down_7|NZ_LT992472.1_282438_282834_-	pfam00436, SSB, Single-strand binding protein family	NA|147aa|down_8|NZ_LT992472.1_283027_283468_+	pfam14183, YwpF, YwpF-like protein	NA|147aa|down_9|NZ_LT992472.1_283524_283965_-	PRK00006, fabZ, 3-hydroxyacyl-ACP dehydratase FabZ
GCF_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	3	330503-330653	3	CRISPRCasFinder	no	csa3,TnsE_C	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Type I-A	AACTTTAGTTGTTAGGGGCTCTTATGCA	28	0	0	NA	NA	NA	2	2	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA|77aa|up_5|NZ_LT992472.1_325375_325606_-,NA|364aa|up_0|NZ_LT992472.1_329393_330485_+,NA|35aa|down_0|NZ_LT992472.1_330982_331087_-,NA|53aa|down_1|NZ_LT992472.1_331766_331925_+,NA|31aa|down_2|NZ_LT992472.1_332360_332453_+	NA|237aa|up_9|NZ_LT992472.1_320985_321696_+	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase	NA|148aa|up_8|NZ_LT992472.1_321816_322260_-	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|138aa|up_7|NZ_LT992472.1_322459_322873_-	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|458aa|up_6|NZ_LT992472.1_323330_324704_-	pfam01878, EVE, EVE domain	NA|77aa|up_5|NZ_LT992472.1_325375_325606_-	NA	NA|313aa|up_4|NZ_LT992472.1_325636_326575_-	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|222aa|up_3|NZ_LT992472.1_327008_327674_-	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	csa3|107aa|up_2|NZ_LT992472.1_327825_328146_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|327aa|up_1|NZ_LT992472.1_328147_329128_+	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	NA|364aa|up_0|NZ_LT992472.1_329393_330485_+	NA	NA|35aa|down_0|NZ_LT992472.1_330982_331087_-	NA	NA|53aa|down_1|NZ_LT992472.1_331766_331925_+	NA	NA|31aa|down_2|NZ_LT992472.1_332360_332453_+	NA	NA|286aa|down_3|NZ_LT992472.1_332582_333440_-	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|261aa|down_4|NZ_LT992472.1_333507_334290_-	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|203aa|down_5|NZ_LT992472.1_334579_335188_-	pfam08937, DUF1863, MTH538 TIR-like domain (DUF1863)	NA|345aa|down_6|NZ_LT992472.1_335215_336250_-	pfam13676, TIR_2, TIR domain	NA|490aa|down_7|NZ_LT992472.1_336343_337813_-	pfam18185, STALD, Sir2- and TIR-associating SLOG family	NA|97aa|down_8|NZ_LT992472.1_337872_338163_-	pfam11867, DUF3387, Domain of unknown function (DUF3387)	TnsE_C|135aa|down_9|NZ_LT992472.1_338287_338692_-	pfam18623, TnsE_C, TnsE C-terminal domain
GCF_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	4	494434-494519	4	CRISPRCasFinder	no	WYL	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Unclear	AAAGTCAGCTTACAATAATGTGCAAGTTGG	30	1	6	494464-494489|494464-494489|494464-494489|494464-494489|494464-494489|494464-494489	NZ_LT992472.1_2614667-2614642|NZ_LT992472.1_285984-286009|NZ_LT992472.1_626380-626355|NZ_LT992472.1_1862996-1863021|NZ_LT992472.1_1907931-1907956|NZ_LT992472.1_2345932-2345957	NA	1	1	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA|65aa|up_6|NZ_LT992472.1_487178_487373_-,NA|78aa|down_1|NZ_LT992472.1_495469_495703_-,NA|110aa|down_8|NZ_LT992472.1_503791_504121_+	NA|248aa|up_9|NZ_LT992472.1_482966_483710_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|652aa|up_8|NZ_LT992472.1_483735_485691_-	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription]	NA|270aa|up_7|NZ_LT992472.1_486300_487110_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|65aa|up_6|NZ_LT992472.1_487178_487373_-	NA	NA|467aa|up_5|NZ_LT992472.1_487546_488947_-	TIGR00931, Uncharacterized_Na+/H+_antiporter_HI_1107, Na+/H+ antiporter NhaC	NA|361aa|up_4|NZ_LT992472.1_489041_490124_-	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	NA|141aa|up_3|NZ_LT992472.1_490371_490794_+	COG3296, COG3296, Uncharacterized protein conserved in bacteria [Function unknown]	NA|167aa|up_2|NZ_LT992472.1_491030_491531_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|318aa|up_1|NZ_LT992472.1_491893_492847_+	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains	NA|375aa|up_0|NZ_LT992472.1_492938_494063_-	PRK06753, PRK06753, hypothetical protein; Provisional	NA|259aa|down_0|NZ_LT992472.1_494671_495448_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|78aa|down_1|NZ_LT992472.1_495469_495703_-	NA	NA|158aa|down_2|NZ_LT992472.1_495997_496471_-	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]	NA|985aa|down_3|NZ_LT992472.1_496470_499425_-	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|316aa|down_4|NZ_LT992472.1_500026_500974_-	PRK09379, PRK09379, LytR family transcriptional regulator	NA|266aa|down_5|NZ_LT992472.1_501106_501904_-	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]	WYL|231aa|down_6|NZ_LT992472.1_502288_502981_+	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	NA|246aa|down_7|NZ_LT992472.1_503005_503743_-	pfam02517, Abi, CAAX protease self-immunity	NA|110aa|down_8|NZ_LT992472.1_503791_504121_+	NA	NA|291aa|down_9|NZ_LT992472.1_504565_505438_+	COG1737, RpiR, Transcriptional regulators [Transcription]
GCF_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	5	670644-670738	5	CRISPRCasFinder	no		csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Orphan	AGGCTCTTATGCAGTTGGTGCGAAGCAA	28	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA|249aa|up_9|NZ_LT992472.1_660229_660976_+,NA|121aa|down_0|NZ_LT992472.1_671406_671769_-,NA|105aa|down_8|NZ_LT992472.1_678581_678896_+	NA|249aa|up_9|NZ_LT992472.1_660229_660976_+	NA	NA|398aa|up_8|NZ_LT992472.1_661199_662393_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|250aa|up_7|NZ_LT992472.1_662404_663154_-	COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|272aa|up_6|NZ_LT992472.1_663146_663962_-	COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|290aa|up_5|NZ_LT992472.1_663958_664828_-	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|312aa|up_4|NZ_LT992472.1_664824_665760_-	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|533aa|up_3|NZ_LT992472.1_665772_667371_-	TIGR02294, Nickel-binding_periplasmic_protein, nickel ABC transporter, nickel/metallophore periplasmic binding protein	NA|434aa|up_2|NZ_LT992472.1_667513_668815_-	COG4408, COG4408, Uncharacterized protein conserved in bacteria [Function unknown]	NA|273aa|up_1|NZ_LT992472.1_668807_669626_-	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family	NA|274aa|up_0|NZ_LT992472.1_669636_670458_-	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]	NA|121aa|down_0|NZ_LT992472.1_671406_671769_-	NA	NA|273aa|down_1|NZ_LT992472.1_672031_672850_-	PRK08589, PRK08589, SDR family oxidoreductase	NA|513aa|down_2|NZ_LT992472.1_673083_674622_+	pfam03806, ABG_transport, AbgT putative transporter family	NA|141aa|down_3|NZ_LT992472.1_674733_675156_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|133aa|down_4|NZ_LT992472.1_675627_676026_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|137aa|down_5|NZ_LT992472.1_676052_676463_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|128aa|down_6|NZ_LT992472.1_676917_677301_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|403aa|down_7|NZ_LT992472.1_677367_678576_+	cd07657, F-BAR_Fes_Fer, The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and Fer (Fes related) tyrosine kinases	NA|105aa|down_8|NZ_LT992472.1_678581_678896_+	NA	NA|140aa|down_9|NZ_LT992472.1_680772_681192_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)
GCF_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	6	698589-698699	6	CRISPRCasFinder	no		csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Orphan	GGTACTTCTGGTGTCGGTGGCGTTGGT	27	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA|89aa|up_2|NZ_LT992472.1_692892_693159_+,NA|103aa|up_1|NZ_LT992472.1_693302_693611_+,NA	NA|452aa|up_9|NZ_LT992472.1_684286_685642_-	cd00519, Lipase_3, Lipase (class 3)	NA|262aa|up_8|NZ_LT992472.1_685638_686424_-	pfam04507, DUF576, Csa1 family	NA|255aa|up_7|NZ_LT992472.1_686671_687436_-	pfam04507, DUF576, Csa1 family	NA|258aa|up_6|NZ_LT992472.1_687547_688321_-	pfam04507, DUF576, Csa1 family	NA|310aa|up_5|NZ_LT992472.1_688563_689493_-	pfam09019, EcoRII-C, EcoRII C terminal	NA|398aa|up_4|NZ_LT992472.1_689588_690782_+	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|584aa|up_3|NZ_LT992472.1_690857_692609_+	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|89aa|up_2|NZ_LT992472.1_692892_693159_+	NA	NA|103aa|up_1|NZ_LT992472.1_693302_693611_+	NA	NA|289aa|up_0|NZ_LT992472.1_693736_694603_-	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|453aa|down_0|NZ_LT992472.1_701839_703198_-	TIGR00791, Gluconate_permease, gluconate transporter	NA|518aa|down_1|NZ_LT992472.1_703314_704868_-	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|226aa|down_2|NZ_LT992472.1_704892_705570_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|255aa|down_3|NZ_LT992472.1_705726_706491_-	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|231aa|down_4|NZ_LT992472.1_706655_707348_-	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|139aa|down_5|NZ_LT992472.1_707578_707995_-	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|608aa|down_6|NZ_LT992472.1_708133_709957_-	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|426aa|down_7|NZ_LT992472.1_710868_712146_-	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|204aa|down_8|NZ_LT992472.1_712692_713304_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|388aa|down_9|NZ_LT992472.1_713401_714565_-	cd17474, MFS_YfmO_like, Bacillus subtilis multidrug efflux protein YfmO and similar transporters of the Major Facilitator Superfamily
GCF_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	7	1243337-1243536	7	CRISPRCasFinder	no		csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Orphan	TGCAAGTTGGCGGGGCCCCAACACAGAAGCT	31	2	2	1243368-1243392|1243424-1243448	NZ_LT992472.1_1243537-1243561|NZ_LT992472.1_285946-285970	NA	3	3	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA,NA|131aa|down_5|NZ_LT992472.1_1248712_1249105_+	NA|574aa|up_9|NZ_LT992472.1_1230783_1232505_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_8|NZ_LT992472.1_1232648_1233323_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|585aa|up_7|NZ_LT992472.1_1233569_1235324_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_6|NZ_LT992472.1_1235326_1236067_+	PRK14084, PRK14084, DNA-binding response regulator	NA|148aa|up_5|NZ_LT992472.1_1236179_1236623_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_4|NZ_LT992472.1_1236615_1237317_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|764aa|up_3|NZ_LT992472.1_1237657_1239949_+	COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]	NA|235aa|up_2|NZ_LT992472.1_1240174_1240879_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|NZ_LT992472.1_1241027_1241819_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|NZ_LT992472.1_1241834_1243271_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|NZ_LT992472.1_1243846_1244608_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|305aa|down_1|NZ_LT992472.1_1244859_1245774_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_2|NZ_LT992472.1_1245801_1246206_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|294aa|down_3|NZ_LT992472.1_1246220_1247102_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_4|NZ_LT992472.1_1247333_1248332_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|131aa|down_5|NZ_LT992472.1_1248712_1249105_+	NA	NA|459aa|down_6|NZ_LT992472.1_1249233_1250610_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_7|NZ_LT992472.1_1250843_1251836_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]	NA|317aa|down_8|NZ_LT992472.1_1252161_1253112_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|220aa|down_9|NZ_LT992472.1_1253163_1253823_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]
GCF_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	8	1610093-1610201	8	CRISPRCasFinder	no		csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Orphan	AAAGGAACGCAGTTGGATGCTACCGCACAACTGCATAAA	39	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA,NA|169aa|down_4|NZ_LT992472.1_1613934_1614441_+,NA|239aa|down_5|NZ_LT992472.1_1614602_1615319_+	NA|209aa|up_9|NZ_LT992472.1_1599597_1600224_+	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|313aa|up_8|NZ_LT992472.1_1600493_1601432_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_7|NZ_LT992472.1_1601877_1602414_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_6|NZ_LT992472.1_1602583_1603060_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_5|NZ_LT992472.1_1603099_1604395_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_4|NZ_LT992472.1_1604422_1604944_+	pfam08741, YwhD, YwhD family	NA|337aa|up_3|NZ_LT992472.1_1605442_1606453_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|139aa|up_2|NZ_LT992472.1_1606728_1607145_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|NZ_LT992472.1_1607141_1608803_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|NZ_LT992472.1_1609287_1609923_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|NZ_LT992472.1_1610252_1611140_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NZ_LT992472.1_1611290_1612241_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NZ_LT992472.1_1612295_1613015_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NZ_LT992472.1_1612998_1613799_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NZ_LT992472.1_1613934_1614441_+	NA	NA|239aa|down_5|NZ_LT992472.1_1614602_1615319_+	NA	NA|263aa|down_6|NZ_LT992472.1_1615487_1616276_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NZ_LT992472.1_1616527_1616902_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NZ_LT992472.1_1617849_1618779_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NZ_LT992472.1_1618971_1619196_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	9	1813917-1813999	9	CRISPRCasFinder	no		csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Orphan	CACCCCAACTCGCATTGCTTGTAGAA	26	1	23	1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973|1813943-1813973	NZ_LT992472.1_131759-131789|NZ_LT992472.1_131869-131899|NZ_LT992472.1_200126-200156|NZ_LT992472.1_1908156-1908126|NZ_LT992472.1_1946957-1946987|NZ_LT992472.1_34000-33970|NZ_LT992472.1_449368-449398|NZ_LT992472.1_494382-494352|NZ_LT992472.1_1225407-1225437|NZ_LT992472.1_1225465-1225495|NZ_LT992472.1_1319149-1319119|NZ_LT992472.1_1601590-1601560|NZ_LT992472.1_1767630-1767600|NZ_LT992472.1_1858844-1858874|NZ_LT992472.1_2040999-2041029|NZ_LT992472.1_2141317-2141287|NZ_LT992472.1_2141371-2141341|NZ_LT992472.1_2734664-2734634|NZ_LT992472.1_895506-895536|NZ_LT992472.1_1822924-1822954|NZ_LT992472.1_1862925-1862895|NZ_LT992472.1_2350261-2350291|NZ_LT992472.1_2396351-2396381	NA	1	1	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA,NA	NA|280aa|up_9|NZ_LT992472.1_1801166_1802006_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|NZ_LT992472.1_1802179_1802830_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|NZ_LT992472.1_1802826_1803063_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|NZ_LT992472.1_1803331_1805317_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|NZ_LT992472.1_1805324_1808171_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|NZ_LT992472.1_1808780_1809713_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|NZ_LT992472.1_1809718_1810558_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|NZ_LT992472.1_1810565_1811051_+	cd04647, LbH_MAT_like, Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins	NA|480aa|up_1|NZ_LT992472.1_1811058_1812498_+	sd00006, TPR, Tetratricopeptide repeat	NA|312aa|up_0|NZ_LT992472.1_1812564_1813500_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|NZ_LT992472.1_1814267_1815179_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|NZ_LT992472.1_1815175_1816171_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|NZ_LT992472.1_1816279_1817224_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|NZ_LT992472.1_1817793_1818381_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|545aa|down_4|NZ_LT992472.1_1818563_1820198_+	PRK13529, PRK13529, oxaloacetate-decarboxylating malate dehydrogenase	NA|301aa|down_5|NZ_LT992472.1_1820404_1821307_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_6|NZ_LT992472.1_1822009_1822639_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_7|NZ_LT992472.1_1823413_1824427_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_8|NZ_LT992472.1_1824479_1825490_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_9|NZ_LT992472.1_1825628_1826819_+	PRK00073, pgk, phosphoglycerate kinase; Provisional
GCF_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	10	1863194-1863274	10	CRISPRCasFinder	no		csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Orphan	TCTTTATCATTTCTGTCCCACTCCC	25	1	1	1863219-1863249	NZ_LT992472.1_1808370-1808340	NA	1	1	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA,NA|105aa|down_7|NZ_LT992472.1_1870880_1871195_-	NA|180aa|up_9|NZ_LT992472.1_1855381_1855921_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_8|NZ_LT992472.1_1856070_1856391_-	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|119aa|up_7|NZ_LT992472.1_1856534_1856891_+	cd03036, ArsC_like, Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC	NA|127aa|up_6|NZ_LT992472.1_1857048_1857429_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_5|NZ_LT992472.1_1857608_1858487_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|up_4|NZ_LT992472.1_1859131_1859518_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|up_3|NZ_LT992472.1_1859510_1859807_+	cd02947, TRX_family, TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains	NA|342aa|up_2|NZ_LT992472.1_1860056_1861082_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|up_1|NZ_LT992472.1_1861074_1861770_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|up_0|NZ_LT992472.1_1861787_1862609_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_0|NZ_LT992472.1_1863416_1863611_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_1|NZ_LT992472.1_1863844_1864696_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_2|NZ_LT992472.1_1865023_1865785_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_3|NZ_LT992472.1_1865883_1867191_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|417aa|down_4|NZ_LT992472.1_1867296_1868547_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|155aa|down_5|NZ_LT992472.1_1868536_1869001_+	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|466aa|down_6|NZ_LT992472.1_1869151_1870549_+	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|105aa|down_7|NZ_LT992472.1_1870880_1871195_-	NA	NA|347aa|down_8|NZ_LT992472.1_1871563_1872604_+	COG4536, CorB, Putative Mg2+ and Co2+ transporter CorB [Inorganic ion transport and metabolism]	NA|356aa|down_9|NZ_LT992472.1_1872617_1873685_+	COG2070, COG2070, Dioxygenases related to 2-nitropropane dioxygenase [General function prediction only]
GCF_900324355.1_10_5235	NZ_LT992472	Staphylococcus aureus isolate 10_5235 chromosome I	11	2737097-2737179	11	CRISPRCasFinder	no		csa3,DEDDh,TnsE_C,WYL,cas3,DinG	Orphan	GAAGCTGACGAAAAAGTCAGCTTAC	25	0	0	NA	NA	NA	1	1	Orphan	csa3,DEDDh,TnsE_C,WYL,cas3,DinG	NA,NA	NA|454aa|up_9|NZ_LT992472.1_2721930_2723292_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|586aa|up_8|NZ_LT992472.1_2723635_2725393_-	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|323aa|up_7|NZ_LT992472.1_2725414_2726383_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|315aa|up_6|NZ_LT992472.1_2726651_2727596_-	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|286aa|up_5|NZ_LT992472.1_2727595_2728453_-	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|410aa|up_4|NZ_LT992472.1_2728647_2729877_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|1066aa|up_3|NZ_LT992472.1_2730325_2733523_-	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|314aa|up_2|NZ_LT992472.1_2733543_2734485_-	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|433aa|up_1|NZ_LT992472.1_2734854_2736153_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|138aa|up_0|NZ_LT992472.1_2736357_2736771_+	pfam00582, Usp, Universal stress protein family	NA|230aa|down_0|NZ_LT992472.1_2737276_2737966_-	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|352aa|down_1|NZ_LT992472.1_2738140_2739196_+	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|373aa|down_2|NZ_LT992472.1_2739511_2740630_-	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|167aa|down_3|NZ_LT992472.1_2740770_2741271_+	pfam00582, Usp, Universal stress protein family	NA|401aa|down_4|NZ_LT992472.1_2741517_2742720_-	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|316aa|down_5|NZ_LT992472.1_2742807_2743755_-	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|165aa|down_6|NZ_LT992472.1_2743877_2744372_-	PRK00522, tpx, thiol peroxidase	NA|257aa|down_7|NZ_LT992472.1_2744469_2745240_-	PRK10621, PRK10621, hypothetical protein; Provisional	NA|408aa|down_8|NZ_LT992472.1_2745283_2746507_-	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional	NA|383aa|down_9|NZ_LT992472.1_2746506_2747655_-	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
