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_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	1	234005-234087	1	CRISPRCasFinder	no		cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Orphan	GAAGCTGACGAAAAAGTCAGCTTAC	25	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA,NA	NA|454aa|up_9|NZ_LT992468.1_218838_220200_+	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|586aa|up_8|NZ_LT992468.1_220543_222301_-	PRK06354, PRK06354, pyruvate kinase; Provisional	NA|323aa|up_7|NZ_LT992468.1_222322_223291_-	PRK03202, PRK03202, ATP-dependent 6-phosphofructokinase	NA|315aa|up_6|NZ_LT992468.1_223559_224504_-	PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated	NA|286aa|up_5|NZ_LT992468.1_224503_225361_-	PRK05654, PRK05654, acetyl-CoA carboxylase carboxyltransferase subunit beta	NA|410aa|up_4|NZ_LT992468.1_225555_226785_-	PRK07232, PRK07232, bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed	NA|1066aa|up_3|NZ_LT992468.1_227233_230431_-	COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]	NA|314aa|up_2|NZ_LT992468.1_230451_231393_-	COG0618, COG0618, Exopolyphosphatase-related proteins [General function prediction only]	NA|433aa|up_1|NZ_LT992468.1_231762_233061_-	COG4109, COG4109, Predicted transcriptional regulator containing CBS domains [Transcription]	NA|138aa|up_0|NZ_LT992468.1_233265_233679_+	pfam00582, Usp, Universal stress protein family	NA|230aa|down_0|NZ_LT992468.1_234184_234874_-	PRK00685, PRK00685, metal-dependent hydrolase; Provisional	NA|352aa|down_1|NZ_LT992468.1_235048_236104_+	COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and metabolism]	NA|373aa|down_2|NZ_LT992468.1_236419_237538_-	cd05305, L-AlaDH, Alanine dehydrogenase NAD-binding and catalytic domains	NA|167aa|down_3|NZ_LT992468.1_237678_238179_+	pfam00582, Usp, Universal stress protein family	NA|401aa|down_4|NZ_LT992468.1_238425_239628_-	PRK00180, PRK00180, acetate kinase A/propionate kinase 2; Reviewed	NA|316aa|down_5|NZ_LT992468.1_239715_240663_-	COG0827, COG0827, Adenine-specific DNA methylase [DNA replication, recombination, and repair]	NA|165aa|down_6|NZ_LT992468.1_240785_241280_-	PRK00522, tpx, thiol peroxidase	NA|257aa|down_7|NZ_LT992468.1_241377_242148_-	PRK10621, PRK10621, hypothetical protein; Provisional	NA|408aa|down_8|NZ_LT992468.1_242191_243415_-	PRK01565, PRK01565, thiamine biosynthesis protein ThiI; Provisional	NA|383aa|down_9|NZ_LT992468.1_243414_244563_-	COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
GCF_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	2	322239-322332	2	CRISPRCasFinder	no	csa3	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Type I-A	GCAATGCGCGTTGGGGTGTGGGGCCCCAACATAG	34	1	1	322273-322298	NZ_LT992468.1_420062-420037	NA	1	1	Orphan	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA|75aa|up_5|NZ_LT992468.1_318332_318557_-,NA|148aa|up_2|NZ_LT992468.1_319768_320212_-,NA|101aa|down_1|NZ_LT992468.1_323466_323769_+	NA|501aa|up_9|NZ_LT992468.1_313364_314867_-	COG4529, COG4529, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|105aa|up_8|NZ_LT992468.1_315509_315824_+	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|431aa|up_7|NZ_LT992468.1_315823_317116_+	PRK15445, PRK15445, arsenical efflux pump membrane protein ArsB	NA|285aa|up_6|NZ_LT992468.1_317202_318057_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|75aa|up_5|NZ_LT992468.1_318332_318557_-	NA	NA|157aa|up_4|NZ_LT992468.1_318755_319226_+	COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]	NA|148aa|up_3|NZ_LT992468.1_319338_319782_+	pfam06338, ComK, ComK protein	NA|148aa|up_2|NZ_LT992468.1_319768_320212_-	NA	NA|212aa|up_1|NZ_LT992468.1_320509_321145_+	pfam02517, Abi, CAAX protease self-immunity	NA|207aa|up_0|NZ_LT992468.1_321311_321932_+	pfam02517, Abi, CAAX protease self-immunity	NA|238aa|down_0|NZ_LT992468.1_322494_323208_-	PRK12376, PRK12376, putative translaldolase; Provisional	NA|101aa|down_1|NZ_LT992468.1_323466_323769_+	NA	NA|122aa|down_2|NZ_LT992468.1_324023_324389_+	PRK14201, PRK14201, fluoride efflux transporter CrcB	NA|118aa|down_3|NZ_LT992468.1_324385_324739_+	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|278aa|down_4|NZ_LT992468.1_324988_325822_-	COG0656, ARA1, Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]	NA|303aa|down_5|NZ_LT992468.1_326033_326942_-	pfam08378, NERD, Nuclease-related domain	NA|398aa|down_6|NZ_LT992468.1_327066_328260_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|531aa|down_7|NZ_LT992468.1_328631_330224_+	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_LT992468.1_330520_331267_-	COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Amino acid transport and metabolism]	NA|158aa|down_9|NZ_LT992468.1_331271_331745_-	TIGR02705, conserved_hypothetical_protein, nucleoside triphosphatase YtkD
GCF_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	3	653753-653965	3	CRISPRCasFinder	no		cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Orphan	TGATGTGCTGTTGTGGAAGCTTGGTGTCGTGCCATGCTACTTTGATG	47	0	0	NA	NA	NA	2	2	Orphan	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA|46aa|up_4|NZ_LT992468.1_650614_650752_-,NA|107aa|down_0|NZ_LT992468.1_653998_654319_+	NA|232aa|up_9|NZ_LT992468.1_643306_644002_+	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_LT992468.1_644354_645875_-	COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]	NA|452aa|up_7|NZ_LT992468.1_646390_647746_-	COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]	NA|357aa|up_6|NZ_LT992468.1_647760_648831_-	PRK01966, ddl, D-alanine--D-alanine ligase	NA|401aa|up_5|NZ_LT992468.1_649148_650351_+	TIGR02210, Rod_shape-determining_protein_RodA, rod shape-determining protein RodA	NA|46aa|up_4|NZ_LT992468.1_650614_650752_-	NA	NA|70aa|up_3|NZ_LT992468.1_650879_651089_-	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_LT992468.1_651100_651394_-	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_LT992468.1_651559_653044_+	TIGR04265, bac_cardiolipin, cardiolipin synthase	NA|216aa|up_0|NZ_LT992468.1_653071_653719_+	COG1418, COG1418, Predicted HD superfamily hydrolase [General function prediction only]	NA|107aa|down_0|NZ_LT992468.1_653998_654319_+	NA	NA|291aa|down_1|NZ_LT992468.1_655960_656833_-	PRK02463, PRK02463, OxaA-like protein precursor; Provisional	NA|214aa|down_2|NZ_LT992468.1_656918_657560_-	PRK00043, thiE, thiamine phosphate synthase	NA|264aa|down_3|NZ_LT992468.1_657561_658353_-	PRK09355, PRK09355, hydroxyethylthiazole kinase; Validated	NA|277aa|down_4|NZ_LT992468.1_658336_659167_-	PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed	NA|230aa|down_5|NZ_LT992468.1_659159_659849_-	TIGR04306, salvage_TenA, thiaminase II	NA|232aa|down_6|NZ_LT992468.1_660235_660931_-	pfam06737, Transglycosylas, Transglycosylase-like domain	NA|132aa|down_7|NZ_LT992468.1_661319_661715_-	pfam00436, SSB, Single-strand binding protein family	NA|147aa|down_8|NZ_LT992468.1_661908_662349_+	pfam14183, YwpF, YwpF-like protein	NA|147aa|down_9|NZ_LT992468.1_662405_662846_-	PRK00006, fabZ, 3-hydroxyacyl-ACP dehydratase FabZ
GCF_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	4	873361-873446	4	CRISPRCasFinder	no	WYL	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Unclear	AAAGTCAGCTTACAATAATGTGCAAGTTGG	30	1	7	873391-873416|873391-873416|873391-873416|873391-873416|873391-873416|873391-873416|873391-873416	NZ_LT992468.1_111826-111801|NZ_LT992468.1_2196790-2196765|NZ_LT992468.1_664865-664890|NZ_LT992468.1_1005307-1005282|NZ_LT992468.1_2200910-2200935|NZ_LT992468.1_2287453-2287478|NZ_LT992468.1_2724316-2724341	NA	1	1	Orphan	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA|65aa|up_6|NZ_LT992468.1_866105_866300_-,NA|78aa|down_1|NZ_LT992468.1_874396_874630_-,NA|110aa|down_8|NZ_LT992468.1_882718_883048_+	NA|248aa|up_9|NZ_LT992468.1_861893_862637_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|652aa|up_8|NZ_LT992468.1_862662_864618_-	COG2207, AraC, AraC-type DNA-binding domain-containing proteins [Transcription]	NA|270aa|up_7|NZ_LT992468.1_865227_866037_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|65aa|up_6|NZ_LT992468.1_866105_866300_-	NA	NA|467aa|up_5|NZ_LT992468.1_866473_867874_-	TIGR00931, Uncharacterized_Na+/H+_antiporter_HI_1107, Na+/H+ antiporter NhaC	NA|361aa|up_4|NZ_LT992468.1_867968_869051_-	pfam02317, Octopine_DH, NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain	NA|141aa|up_3|NZ_LT992468.1_869298_869721_+	COG3296, COG3296, Uncharacterized protein conserved in bacteria [Function unknown]	NA|167aa|up_2|NZ_LT992468.1_869957_870458_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|318aa|up_1|NZ_LT992468.1_870820_871774_+	cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains	NA|375aa|up_0|NZ_LT992468.1_871865_872990_-	PRK06753, PRK06753, hypothetical protein; Provisional	NA|259aa|down_0|NZ_LT992468.1_873598_874375_-	COG4193, LytD, Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]	NA|78aa|down_1|NZ_LT992468.1_874396_874630_-	NA	NA|158aa|down_2|NZ_LT992468.1_874924_875398_-	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]	NA|985aa|down_3|NZ_LT992468.1_875397_878352_-	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|316aa|down_4|NZ_LT992468.1_878953_879901_-	PRK09379, PRK09379, LytR family transcriptional regulator	NA|266aa|down_5|NZ_LT992468.1_880033_880831_-	COG0483, SuhB, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family [Carbohydrate transport and metabolism]	WYL|231aa|down_6|NZ_LT992468.1_881215_881908_+	COG2378, COG2378, Predicted transcriptional regulator [Transcription]	NA|246aa|down_7|NZ_LT992468.1_881932_882670_-	pfam02517, Abi, CAAX protease self-immunity	NA|110aa|down_8|NZ_LT992468.1_882718_883048_+	NA	NA|291aa|down_9|NZ_LT992468.1_883492_884365_+	COG1737, RpiR, Transcriptional regulators [Transcription]
GCF_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	5	1049571-1049665	5	CRISPRCasFinder	no		cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Orphan	AGGCTCTTATGCAGTTGGTGCGAAGCAA	28	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA|249aa|up_9|NZ_LT992468.1_1039156_1039903_+,NA|121aa|down_0|NZ_LT992468.1_1050333_1050696_-,NA|105aa|down_8|NZ_LT992468.1_1057508_1057823_+	NA|249aa|up_9|NZ_LT992468.1_1039156_1039903_+	NA	NA|398aa|up_8|NZ_LT992468.1_1040126_1041320_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|250aa|up_7|NZ_LT992468.1_1041331_1042081_-	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_LT992468.1_1042073_1042889_-	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_LT992468.1_1042885_1043755_-	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_LT992468.1_1043751_1044687_-	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_LT992468.1_1044699_1046298_-	TIGR02294, Nickel-binding_periplasmic_protein, nickel ABC transporter, nickel/metallophore periplasmic binding protein	NA|434aa|up_2|NZ_LT992468.1_1046440_1047742_-	COG4408, COG4408, Uncharacterized protein conserved in bacteria [Function unknown]	NA|273aa|up_1|NZ_LT992468.1_1047734_1048553_-	cd08261, Zn_ADH7, Alcohol dehydrogenases of the MDR family	NA|274aa|up_0|NZ_LT992468.1_1048563_1049385_-	COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and metabolism]	NA|121aa|down_0|NZ_LT992468.1_1050333_1050696_-	NA	NA|273aa|down_1|NZ_LT992468.1_1050958_1051777_-	PRK08589, PRK08589, SDR family oxidoreductase	NA|513aa|down_2|NZ_LT992468.1_1052010_1053549_+	pfam03806, ABG_transport, AbgT putative transporter family	NA|141aa|down_3|NZ_LT992468.1_1053660_1054083_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|133aa|down_4|NZ_LT992468.1_1054554_1054953_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|137aa|down_5|NZ_LT992468.1_1054979_1055390_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|128aa|down_6|NZ_LT992468.1_1055844_1056228_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)	NA|403aa|down_7|NZ_LT992468.1_1056294_1057503_+	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_LT992468.1_1057508_1057823_+	NA	NA|140aa|down_9|NZ_LT992468.1_1059699_1060119_-	pfam07252, DUF1433, Protein of unknown function (DUF1433)
GCF_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	6	1077516-1077626	6	CRISPRCasFinder	no		cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Orphan	GGTACTTCTGGTGTCGGTGGCGTTGGT	27	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA|89aa|up_2|NZ_LT992468.1_1071819_1072086_+,NA|103aa|up_1|NZ_LT992468.1_1072229_1072538_+,NA	NA|452aa|up_9|NZ_LT992468.1_1063213_1064569_-	cd00519, Lipase_3, Lipase (class 3)	NA|262aa|up_8|NZ_LT992468.1_1064565_1065351_-	pfam04507, DUF576, Csa1 family	NA|255aa|up_7|NZ_LT992468.1_1065598_1066363_-	pfam04507, DUF576, Csa1 family	NA|258aa|up_6|NZ_LT992468.1_1066474_1067248_-	pfam04507, DUF576, Csa1 family	NA|310aa|up_5|NZ_LT992468.1_1067490_1068420_-	pfam09019, EcoRII-C, EcoRII C terminal	NA|398aa|up_4|NZ_LT992468.1_1068515_1069709_+	TIGR00675, Modification_methylase, DNA-methyltransferase (dcm)	NA|584aa|up_3|NZ_LT992468.1_1069784_1071536_+	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|89aa|up_2|NZ_LT992468.1_1071819_1072086_+	NA	NA|103aa|up_1|NZ_LT992468.1_1072229_1072538_+	NA	NA|289aa|up_0|NZ_LT992468.1_1072663_1073530_-	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|453aa|down_0|NZ_LT992468.1_1080766_1082125_-	TIGR00791, Gluconate_permease, gluconate transporter	NA|518aa|down_1|NZ_LT992468.1_1082241_1083795_-	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|226aa|down_2|NZ_LT992468.1_1083819_1084497_-	COG1802, GntR, Transcriptional regulators [Transcription]	NA|255aa|down_3|NZ_LT992468.1_1084653_1085418_-	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|231aa|down_4|NZ_LT992468.1_1085582_1086275_-	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|139aa|down_5|NZ_LT992468.1_1086505_1086922_-	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|608aa|down_6|NZ_LT992468.1_1087060_1088884_-	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|426aa|down_7|NZ_LT992468.1_1089795_1091073_-	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|204aa|down_8|NZ_LT992468.1_1091619_1092231_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|388aa|down_9|NZ_LT992468.1_1092328_1093492_-	cd17474, MFS_YfmO_like, Bacillus subtilis multidrug efflux protein YfmO and similar transporters of the Major Facilitator Superfamily
GCF_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	7	1622090-1622289	7	CRISPRCasFinder	no		cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Orphan	TGCAAGTTGGCGGGGCCCCAACACAGAAGCT	31	2	2	1622121-1622145|1622177-1622201	NZ_LT992468.1_1622290-1622314|NZ_LT992468.1_664827-664851	NA	3	3	Orphan	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA,NA|131aa|down_5|NZ_LT992468.1_1627465_1627858_+	NA|574aa|up_9|NZ_LT992468.1_1609536_1611258_+	pfam18674, TarS_C1, TarS beta-glycosyltransferase C-terminal domain 1	NA|225aa|up_8|NZ_LT992468.1_1611401_1612076_+	PRK13276, PRK13276, iron-sulfur cluster repair di-iron protein ScdA	NA|585aa|up_7|NZ_LT992468.1_1612322_1614077_+	COG3275, LytS, Putative regulator of cell autolysis [Signal transduction mechanisms]	NA|247aa|up_6|NZ_LT992468.1_1614079_1614820_+	PRK14084, PRK14084, DNA-binding response regulator	NA|148aa|up_5|NZ_LT992468.1_1614932_1615376_+	PRK04125, PRK04125, antiholin-like protein LrgA	NA|234aa|up_4|NZ_LT992468.1_1615368_1616070_+	PRK04288, PRK04288, antiholin-like protein LrgB; Provisional	NA|764aa|up_3|NZ_LT992468.1_1616410_1618702_+	COG3256, NorB, Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]	NA|235aa|up_2|NZ_LT992468.1_1618927_1619632_-	COG2188, PhnF, Transcriptional regulators [Transcription]	NA|264aa|up_1|NZ_LT992468.1_1619780_1620572_+	COG2190, NagE, Phosphotransferase system IIA components [Carbohydrate transport and metabolism]	NA|479aa|up_0|NZ_LT992468.1_1620587_1622024_+	PRK09589, celA, 6-phospho-beta-glucosidase; Reviewed	NA|254aa|down_0|NZ_LT992468.1_1622599_1623361_-	pfam13649, Methyltransf_25, Methyltransferase domain	NA|305aa|down_1|NZ_LT992468.1_1623612_1624527_-	TIGR02152, Putative_ribokinase, ribokinase	NA|135aa|down_2|NZ_LT992468.1_1624554_1624959_-	PRK11797, PRK11797, D-ribose pyranase; Provisional	NA|294aa|down_3|NZ_LT992468.1_1624973_1625855_-	pfam06800, Sugar_transport, Sugar transport protein	NA|333aa|down_4|NZ_LT992468.1_1626086_1627085_-	COG1609, PurR, Transcriptional regulators [Transcription]	NA|131aa|down_5|NZ_LT992468.1_1627465_1627858_+	NA	NA|459aa|down_6|NZ_LT992468.1_1627986_1629363_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|331aa|down_7|NZ_LT992468.1_1629596_1630589_+	COG3049, COG3049, Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]	NA|317aa|down_8|NZ_LT992468.1_1630914_1631865_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|220aa|down_9|NZ_LT992468.1_1631916_1632576_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]
GCF_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	8	1989622-1989730	8	CRISPRCasFinder	no		cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Orphan	AAAGGAACGCAGTTGGATGCTACCGCACAACTGCATAAA	39	0	0	NA	NA	NA	1	1	Orphan	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA,NA|169aa|down_4|NZ_LT992468.1_1993463_1993970_+,NA|239aa|down_5|NZ_LT992468.1_1994131_1994848_+	NA|209aa|up_9|NZ_LT992468.1_1979126_1979753_+	pfam04276, DUF443, Protein of unknown function (DUF443)	NA|313aa|up_8|NZ_LT992468.1_1980022_1980961_+	cd19083, AKR_AKR11A1_11D1, AKR11A and  AKR11D families of aldo-keto reductase (AKR)	NA|179aa|up_7|NZ_LT992468.1_1981406_1981943_+	COG0655, WrbA, Multimeric flavodoxin WrbA [General function prediction only]	NA|159aa|up_6|NZ_LT992468.1_1982112_1982589_+	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|432aa|up_5|NZ_LT992468.1_1982628_1983924_+	COG1078, COG1078, HD superfamily phosphohydrolases [General function prediction only]	NA|174aa|up_4|NZ_LT992468.1_1983951_1984473_+	pfam08741, YwhD, YwhD family	NA|337aa|up_3|NZ_LT992468.1_1984971_1985982_+	PRK09422, PRK09422, ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional	NA|139aa|up_2|NZ_LT992468.1_1986257_1986674_+	COG4506, COG4506, Uncharacterized protein conserved in bacteria [Function unknown]	NA|554aa|up_1|NZ_LT992468.1_1986670_1988332_+	PRK01611, argS, arginyl-tRNA synthetase; Reviewed	NA|212aa|up_0|NZ_LT992468.1_1988816_1989452_+	COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]	NA|296aa|down_0|NZ_LT992468.1_1989781_1990669_+	cd01143, YvrC, Periplasmic binding protein YvrC	NA|317aa|down_1|NZ_LT992468.1_1990819_1991770_+	pfam01032, FecCD, FecCD transport family	NA|240aa|down_2|NZ_LT992468.1_1991824_1992544_+	COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General function prediction only]	NA|267aa|down_3|NZ_LT992468.1_1992527_1993328_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|169aa|down_4|NZ_LT992468.1_1993463_1993970_+	NA	NA|239aa|down_5|NZ_LT992468.1_1994131_1994848_+	NA	NA|263aa|down_6|NZ_LT992468.1_1995016_1995805_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|125aa|down_7|NZ_LT992468.1_1996056_1996431_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|310aa|down_8|NZ_LT992468.1_1997378_1998308_-	COG3238, COG3238, Uncharacterized protein conserved in bacteria [Function unknown]	NA|75aa|down_9|NZ_LT992468.1_1998500_1998725_-	pfam11148, DUF2922, Protein of unknown function (DUF2922)
GCF_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	9	2151840-2151922	9	CRISPRCasFinder	no		cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Orphan	CACCCCAACTCGCATTGCTTGTAGAA	26	1	25	2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896|2151866-2151896	NZ_LT992468.1_419990-420020|NZ_LT992468.1_420100-420130|NZ_LT992468.1_579006-579036|NZ_LT992468.1_2287678-2287648|NZ_LT992468.1_2326479-2326509|NZ_LT992468.1_231572-231542|NZ_LT992468.1_322230-322200|NZ_LT992468.1_828185-828215|NZ_LT992468.1_873309-873279|NZ_LT992468.1_1604160-1604190|NZ_LT992468.1_1604218-1604248|NZ_LT992468.1_1697902-1697872|NZ_LT992468.1_1981119-1981089|NZ_LT992468.1_2105553-2105523|NZ_LT992468.1_2196701-2196731|NZ_LT992468.1_2419446-2419476|NZ_LT992468.1_2519764-2519734|NZ_LT992468.1_2519818-2519788|NZ_LT992468.1_838933-838963|NZ_LT992468.1_838988-839018|NZ_LT992468.1_1274259-1274289|NZ_LT992468.1_2160847-2160877|NZ_LT992468.1_2200839-2200809|NZ_LT992468.1_2728645-2728675|NZ_LT992468.1_2774735-2774765	NA	1	1	Orphan	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA,NA	NA|280aa|up_9|NZ_LT992468.1_2139089_2139929_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|NZ_LT992468.1_2140102_2140753_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|NZ_LT992468.1_2140749_2140986_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|NZ_LT992468.1_2141254_2143240_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|949aa|up_5|NZ_LT992468.1_2143247_2146094_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|NZ_LT992468.1_2146703_2147636_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|NZ_LT992468.1_2147641_2148481_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|NZ_LT992468.1_2148488_2148974_+	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_LT992468.1_2148981_2150421_+	sd00006, TPR, Tetratricopeptide repeat	NA|312aa|up_0|NZ_LT992468.1_2150487_2151423_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|NZ_LT992468.1_2152190_2153102_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|NZ_LT992468.1_2153098_2154094_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|NZ_LT992468.1_2154202_2155147_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|NZ_LT992468.1_2155716_2156304_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|545aa|down_4|NZ_LT992468.1_2156486_2158121_+	PRK13529, PRK13529, oxaloacetate-decarboxylating malate dehydrogenase	NA|301aa|down_5|NZ_LT992468.1_2158327_2159230_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_6|NZ_LT992468.1_2159932_2160562_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_7|NZ_LT992468.1_2161336_2162350_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_8|NZ_LT992468.1_2162402_2163413_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_9|NZ_LT992468.1_2163551_2164742_+	PRK00073, pgk, phosphoglycerate kinase; Provisional
GCF_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	10	2201108-2201188	10	CRISPRCasFinder	no		cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Orphan	TCTTTATCATTTCTGTCCCACTCCC	25	1	1	2201133-2201163	NZ_LT992468.1_2146293-2146263	NA	1	1	Orphan	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA,NA|81aa|down_8|NZ_LT992468.1_2209646_2209889_-	NA|180aa|up_9|NZ_LT992468.1_2193238_2193778_+	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|107aa|up_8|NZ_LT992468.1_2193927_2194248_-	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_LT992468.1_2194391_2194748_+	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_LT992468.1_2194905_2195286_+	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|293aa|up_5|NZ_LT992468.1_2195465_2196344_+	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|129aa|up_4|NZ_LT992468.1_2197045_2197432_+	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|99aa|up_3|NZ_LT992468.1_2197424_2197721_+	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_LT992468.1_2197970_2198996_+	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|232aa|up_1|NZ_LT992468.1_2198988_2199684_+	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|274aa|up_0|NZ_LT992468.1_2199701_2200523_+	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|65aa|down_0|NZ_LT992468.1_2201330_2201525_+	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|284aa|down_1|NZ_LT992468.1_2201758_2202610_-	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|254aa|down_2|NZ_LT992468.1_2202937_2203699_+	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|436aa|down_3|NZ_LT992468.1_2203797_2205105_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|417aa|down_4|NZ_LT992468.1_2205210_2206461_+	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|155aa|down_5|NZ_LT992468.1_2206450_2206915_+	TIGR01994, Iron-sulfur_cluster_assembly_scaffold_protein_IscU, SUF system FeS assembly protein, NifU family	NA|466aa|down_6|NZ_LT992468.1_2207065_2208463_+	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|350aa|down_7|NZ_LT992468.1_2208530_2209580_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|81aa|down_8|NZ_LT992468.1_2209646_2209889_-	NA	NA|328aa|down_9|NZ_LT992468.1_2209899_2210883_-	pfam00535, Glycos_transf_2, Glycosyl transferase family 2
GCF_900324315.1_12_LA_293	NZ_LT992468	Staphylococcus aureus isolate 12_LA_293 chromosome I	11	2592239-2592331	11	CRISPRCasFinder	no	cas3	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	Unclear	TAAGAAACACTAATCAATAAATTGATAACT	30	0	0	NA	NA	NA	1	1	Unclear	cas3,csa3,DEDDh,TnsE_C,WYL,DinG	NA,NA	NA|215aa|up_9|NZ_LT992468.1_2581951_2582596_+	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]	NA|214aa|up_8|NZ_LT992468.1_2582602_2583244_+	COG1564, THI80, Thiamine pyrophosphokinase [Coenzyme metabolism]	NA|63aa|up_7|NZ_LT992468.1_2583624_2583813_-	PRK00359, rpmB, 50S ribosomal protein L28; Reviewed	NA|125aa|up_6|NZ_LT992468.1_2584255_2584630_+	COG1302, COG1302, Uncharacterized protein conserved in bacteria [Function unknown]	NA|549aa|up_5|NZ_LT992468.1_2584644_2586291_+	COG1461, COG1461, Predicted kinase related to dihydroxyacetone kinase [General function prediction only]	cas3|687aa|up_4|NZ_LT992468.1_2586480_2588541_+	PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional	NA|191aa|up_3|NZ_LT992468.1_2588743_2589316_+	PRK04424, PRK04424, transcription factor FapR	NA|329aa|up_2|NZ_LT992468.1_2589320_2590307_+	PRK05331, PRK05331, phosphate acyltransferase PlsX	NA|309aa|up_1|NZ_LT992468.1_2590299_2591226_+	COG0331, FabD, (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]	NA|245aa|up_0|NZ_LT992468.1_2591218_2591953_+	PRK05557, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Validated	NA|78aa|down_0|NZ_LT992468.1_2592420_2592654_+	PRK00982, acpP, acyl carrier protein; Provisional	NA|244aa|down_1|NZ_LT992468.1_2592769_2593501_+	PRK00102, rnc, ribonuclease III; Reviewed	NA|1189aa|down_2|NZ_LT992468.1_2593647_2597214_+	COG1196, Smc, Chromosome segregation ATPases [Cell division and chromosome partitioning]	NA|417aa|down_3|NZ_LT992468.1_2597213_2598464_+	PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional	NA|111aa|down_4|NZ_LT992468.1_2598450_2598783_+	PRK00118, PRK00118, putative DNA-binding protein; Validated	NA|456aa|down_5|NZ_LT992468.1_2598808_2600176_+	PRK10867, PRK10867, signal recognition particle protein; Provisional	NA|92aa|down_6|NZ_LT992468.1_2600610_2600886_+	COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]	NA|168aa|down_7|NZ_LT992468.1_2601073_2601577_+	PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional	NA|246aa|down_8|NZ_LT992468.1_2601576_2602314_+	PRK00026, trmD, tRNA (guanine-N(1)-)-methyltransferase; Reviewed	NA|117aa|down_9|NZ_LT992468.1_2602416_2602767_+	PRK05338, rplS, 50S ribosomal protein L19; Provisional
