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_009912895.1_ASM991289v1	NZ_CP047856	Staphylococcus aureus strain UP_1435 chromosome, complete genome	1	410980-411064	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TTCTACAGGCAATGCAAGTTGGGGTG	26	1	2	411006-411038|411006-411038	NZ_CP047856.1_681012-680980|NZ_CP047856.1_1242963-1242995	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA	NA|190aa|up_9|NZ_CP047856.1_401609_402179_+	TIGR00482, Probable_nicotinate-nucleotide_adenylyltransferase, nicotinate (nicotinamide) nucleotide adenylyltransferase	NA|195aa|up_8|NZ_CP047856.1_402168_402753_+	COG1713, COG1713, Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism]	NA|118aa|up_7|NZ_CP047856.1_402753_403107_+	COG0799, COG0799, Uncharacterized homolog of plant Iojap protein [Function unknown]	NA|239aa|up_6|NZ_CP047856.1_403109_403826_+	pfam13649, Methyltransf_25, Methyltransferase domain	NA|229aa|up_5|NZ_CP047856.1_403865_404552_+	COG1555, ComEA, DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]	NA|154aa|up_4|NZ_CP047856.1_404643_405105_+	TIGR02571, putative_dCMP_deaminase, ComE operon protein 2	NA|716aa|up_3|NZ_CP047856.1_405163_407311_+	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|325aa|up_2|NZ_CP047856.1_407367_408342_+	PRK05574, holA, DNA polymerase III subunit delta; Reviewed	NA|84aa|up_1|NZ_CP047856.1_408386_408638_-	PRK00239, rpsT, 30S ribosomal protein S20; Reviewed	NA|608aa|up_0|NZ_CP047856.1_408983_410807_+	PRK05433, PRK05433, GTP-binding protein LepA; Provisional	NA|375aa|down_0|NZ_CP047856.1_411372_412497_+	PRK08599, PRK08599, oxygen-independent coproporphyrinogen III oxidase	NA|326aa|down_1|NZ_CP047856.1_412597_413575_+	TIGR00331, Heat-inducible_transcription_repressor_HrcA, heat shock gene repressor HrcA	NA|209aa|down_2|NZ_CP047856.1_413606_414233_+	PRK14140, PRK14140, heat shock protein GrpE; Provisional	NA|611aa|down_3|NZ_CP047856.1_414301_416134_+	PRK00290, dnaK, molecular chaperone DnaK; Provisional	NA|380aa|down_4|NZ_CP047856.1_416269_417409_+	PRK14280, PRK14280, molecular chaperone DnaJ	NA|313aa|down_5|NZ_CP047856.1_417412_418351_+	pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA)	NA|251aa|down_6|NZ_CP047856.1_418352_419105_+	COG1385, COG1385, Uncharacterized protein conserved in bacteria [Function unknown]	NA|449aa|down_7|NZ_CP047856.1_419111_420458_+	COG0621, MiaB, 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]	NA|59aa|down_8|NZ_CP047856.1_420750_420927_+	PRK00270, rpsU, 30S ribosomal protein S21; Reviewed	NA|228aa|down_9|NZ_CP047856.1_421170_421854_+	COG1030, NfeD, Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
GCF_009912895.1_ASM991289v1	NZ_CP047856	Staphylococcus aureus strain UP_1435 chromosome, complete genome	2	1199735-1199816	2	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TTCTACAGGCAATGCAAGTTGGGG	24	1	1	1199759-1199792	NZ_CP047856.1_681013-680980	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|38aa|down_1|NZ_CP047856.1_1200799_1200913_-	NA|414aa|up_9|NZ_CP047856.1_1190162_1191404_-	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|436aa|up_8|NZ_CP047856.1_1191518_1192826_-	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|254aa|up_7|NZ_CP047856.1_1192923_1193685_-	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|284aa|up_6|NZ_CP047856.1_1194012_1194864_+	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|65aa|up_5|NZ_CP047856.1_1195097_1195292_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|274aa|up_4|NZ_CP047856.1_1195645_1196467_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|232aa|up_3|NZ_CP047856.1_1196484_1197180_-	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|342aa|up_2|NZ_CP047856.1_1197172_1198198_-	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|99aa|up_1|NZ_CP047856.1_1198447_1198744_-	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|129aa|up_0|NZ_CP047856.1_1198736_1199123_-	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|293aa|down_0|NZ_CP047856.1_1199919_1200798_-	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|38aa|down_1|NZ_CP047856.1_1200799_1200913_-	NA	NA|127aa|down_2|NZ_CP047856.1_1200976_1201357_-	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|119aa|down_3|NZ_CP047856.1_1201514_1201871_-	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|107aa|down_4|NZ_CP047856.1_1202014_1202335_+	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|180aa|down_5|NZ_CP047856.1_1202485_1203025_-	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|239aa|down_6|NZ_CP047856.1_1203107_1203824_-	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|141aa|down_7|NZ_CP047856.1_1203971_1204394_+	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|165aa|down_8|NZ_CP047856.1_1204792_1205287_+	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|206aa|down_9|NZ_CP047856.1_1205441_1206059_+	COG1279, COG1279, Lysine efflux permease [General function prediction only]
GCF_009912895.1_ASM991289v1	NZ_CP047856	Staphylococcus aureus strain UP_1435 chromosome, complete genome	3	1248475-1248553	3	CRISPRCasFinder	no	cas3	DEDDh,csa3,cas3,DinG,WYL,RT	Unclear	AGAATTTCGAAAAGAAATTCTACA	24	1	3	1248499-1248529|1248499-1248529|1248499-1248529	NZ_CP047856.1_1804970-1804940|NZ_CP047856.1_376551-376581|NZ_CP047856.1_1805025-1804995	NA	1	1	Unclear	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|36aa|down_5|NZ_CP047856.1_1256031_1256139_-,NA|35aa|down_7|NZ_CP047856.1_1257571_1257676_-	NA|301aa|up_9|NZ_CP047856.1_1237356_1238259_+	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|196aa|up_8|NZ_CP047856.1_1238501_1239089_-	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|315aa|up_7|NZ_CP047856.1_1239652_1240597_-	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|332aa|up_6|NZ_CP047856.1_1240707_1241703_-	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|304aa|up_5|NZ_CP047856.1_1241699_1242611_-	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|312aa|up_4|NZ_CP047856.1_1243496_1244432_-	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|480aa|up_3|NZ_CP047856.1_1244498_1245938_-	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|162aa|up_2|NZ_CP047856.1_1245945_1246431_-	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|280aa|up_1|NZ_CP047856.1_1246438_1247278_-	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|311aa|up_0|NZ_CP047856.1_1247283_1248216_-	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|949aa|down_0|NZ_CP047856.1_1248879_1251726_-	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|662aa|down_1|NZ_CP047856.1_1251733_1253719_-	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|79aa|down_2|NZ_CP047856.1_1253987_1254224_-	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|217aa|down_3|NZ_CP047856.1_1254220_1254871_-	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|280aa|down_4|NZ_CP047856.1_1255044_1255884_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|36aa|down_5|NZ_CP047856.1_1256031_1256139_-	NA	NA|370aa|down_6|NZ_CP047856.1_1256292_1257403_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|35aa|down_7|NZ_CP047856.1_1257571_1257676_-	NA	NA|844aa|down_8|NZ_CP047856.1_1257717_1260249_-	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|191aa|down_9|NZ_CP047856.1_1260662_1261235_-	COG1544, COG1544, Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
GCF_009912895.1_ASM991289v1	NZ_CP047856	Staphylococcus aureus strain UP_1435 chromosome, complete genome	4	1644864-1644966	4	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	CAAATTTAATACTCAATTCATATA	24	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|179aa|up_7|NZ_CP047856.1_1636482_1637019_+,NA|221aa|up_1|NZ_CP047856.1_1643110_1643773_+,NA|33aa|down_0|NZ_CP047856.1_1645641_1645740_-,NA|128aa|down_6|NZ_CP047856.1_1651987_1652371_+,NA|70aa|down_8|NZ_CP047856.1_1653195_1653405_+	NA|91aa|up_9|NZ_CP047856.1_1634715_1634988_+	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|235aa|up_8|NZ_CP047856.1_1635386_1636091_+	pfam02452, PemK_toxin, PemK-like, MazF-like toxin of type II toxin-antitoxin system	NA|179aa|up_7|NZ_CP047856.1_1636482_1637019_+	NA	NA|514aa|up_6|NZ_CP047856.1_1637131_1638673_-	PRK00074, guaA, GMP synthase; Reviewed	NA|489aa|up_5|NZ_CP047856.1_1638697_1640164_-	PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase; Reviewed	NA|423aa|up_4|NZ_CP047856.1_1640201_1641470_-	TIGR03173, pbuX, xanthine permease	NA|193aa|up_3|NZ_CP047856.1_1641469_1642048_-	PRK09219, PRK09219, xanthine phosphoribosyltransferase; Validated	NA|136aa|up_2|NZ_CP047856.1_1642560_1642968_+	pfam11181, YflT, Heat induced stress protein YflT	NA|221aa|up_1|NZ_CP047856.1_1643110_1643773_+	NA	NA|319aa|up_0|NZ_CP047856.1_1643890_1644847_+	TIGR02168, Chromosome_partition_protein_Smc, chromosome segregation protein SMC, common bacterial type	NA|33aa|down_0|NZ_CP047856.1_1645641_1645740_-	NA	NA|463aa|down_1|NZ_CP047856.1_1645824_1647213_+	COG1823, COG1823, Predicted Na+/dicarboxylate symporter [General function prediction only]	NA|252aa|down_2|NZ_CP047856.1_1647292_1648048_-	cd02146, NfsA-like, nitroreductase similar to Escherichia coli NfsA	NA|190aa|down_3|NZ_CP047856.1_1648539_1649109_+	TIGR03137, AhpC, peroxiredoxin	NA|508aa|down_4|NZ_CP047856.1_1649124_1650648_+	PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F; Provisional	NA|209aa|down_5|NZ_CP047856.1_1651091_1651718_+	NF033193, lipo_NDxxF, NDxxF motif lipoprotein	NA|128aa|down_6|NZ_CP047856.1_1651987_1652371_+	NA	NA|194aa|down_7|NZ_CP047856.1_1652436_1653018_-	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|70aa|down_8|NZ_CP047856.1_1653195_1653405_+	NA	NA|84aa|down_9|NZ_CP047856.1_1653443_1653695_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_009912895.1_ASM991289v1	NZ_CP047856	Staphylococcus aureus strain UP_1435 chromosome, complete genome	5	2355459-2355592	1	PILER-CR	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TATTGAAGAAGATACAA	17	2	2	2355476-2355521|2355539-2355575	NZ_CP047856.1_2351952-2351997|NZ_CP047856.1_2352015-2352051	NA	2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|67aa|up_1|NZ_CP047856.1_2349128_2349329_+,NA|78aa|down_5|NZ_CP047856.1_2363909_2364143_+,NA|103aa|down_6|NZ_CP047856.1_2364250_2364559_-,NA|89aa|down_7|NZ_CP047856.1_2364702_2364969_-	NA|426aa|up_9|NZ_CP047856.1_2339125_2340403_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_8|NZ_CP047856.1_2340879_2342703_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_7|NZ_CP047856.1_2342841_2343258_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_6|NZ_CP047856.1_2343488_2344181_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|255aa|up_5|NZ_CP047856.1_2344345_2345110_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_4|NZ_CP047856.1_2345262_2345943_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_3|NZ_CP047856.1_2345966_2347520_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_2|NZ_CP047856.1_2347636_2348995_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|67aa|up_1|NZ_CP047856.1_2349128_2349329_+	NA	NA|997aa|up_0|NZ_CP047856.1_2349463_2352454_+	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|289aa|down_0|NZ_CP047856.1_2356200_2357067_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|248aa|down_1|NZ_CP047856.1_2357277_2358021_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|119aa|down_2|NZ_CP047856.1_2358344_2358701_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|1116aa|down_3|NZ_CP047856.1_2359005_2362353_+	pfam18483, Bact_lectin, Bacterial lectin	NA|359aa|down_4|NZ_CP047856.1_2362736_2363813_+	cd06173, MFS_MefA_like, Macrolide efflux protein A and similar proteins of the Major Facilitator Superfamily of transporters	NA|78aa|down_5|NZ_CP047856.1_2363909_2364143_+	NA	NA|103aa|down_6|NZ_CP047856.1_2364250_2364559_-	NA	NA|89aa|down_7|NZ_CP047856.1_2364702_2364969_-	NA	NA|603aa|down_8|NZ_CP047856.1_2365252_2367061_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_9|NZ_CP047856.1_2367192_2367585_+	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)
GCF_009912895.1_ASM991289v1	NZ_CP047856	Staphylococcus aureus strain UP_1435 chromosome, complete genome	6	2431006-2431084	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TGCAAGTTGGCGGGGCCCCAACA	23	1	5	2431029-2431061|2431029-2431061|2431029-2431061|2431029-2431061|2431029-2431061	NZ_CP047856.1_1199446-1199478|NZ_CP047856.1_1235664-1235696|NZ_CP047856.1_2822753-2822721|NZ_CP047856.1_1235720-1235752|NZ_CP047856.1_1235776-1235808	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|220aa|up_3|NZ_CP047856.1_2427930_2428590_-,NA|36aa|up_0|NZ_CP047856.1_2430579_2430687_+,NA	NA|693aa|up_9|NZ_CP047856.1_2420392_2422471_-	COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]	NA|470aa|up_8|NZ_CP047856.1_2422608_2424018_-	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|269aa|up_7|NZ_CP047856.1_2424303_2425110_+	TIGR03729, acc_ester, putative phosphoesterase	NA|219aa|up_6|NZ_CP047856.1_2425172_2425829_-	COG4990, COG4990, Uncharacterized protein conserved in bacteria [Function unknown]	NA|158aa|up_5|NZ_CP047856.1_2425941_2426415_+	COG3708, COG3708, Uncharacterized protein conserved in bacteria [Function unknown]	NA|404aa|up_4|NZ_CP047856.1_2426537_2427749_-	cd17320, MFS_MdfA_MDR_like, Multidrug transporter MdfA and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|220aa|up_3|NZ_CP047856.1_2427930_2428590_-	NA	NA|381aa|up_2|NZ_CP047856.1_2428649_2429792_-	TIGR00045, Glycerate_kinase, glycerate kinase	NA|129aa|up_1|NZ_CP047856.1_2430059_2430446_+	COG2246, COG2246, Predicted membrane protein [Function unknown]	NA|36aa|up_0|NZ_CP047856.1_2430579_2430687_+	NA	NA|588aa|down_0|NZ_CP047856.1_2431389_2433153_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|578aa|down_1|NZ_CP047856.1_2433177_2434911_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|229aa|down_2|NZ_CP047856.1_2435363_2436050_+	COG0132, BioD, Dethiobiotin synthetase [Coenzyme metabolism]	NA|453aa|down_3|NZ_CP047856.1_2436027_2437386_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|down_4|NZ_CP047856.1_2437387_2438395_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|down_5|NZ_CP047856.1_2438372_2439488_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|down_6|NZ_CP047856.1_2439498_2440191_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|down_7|NZ_CP047856.1_2440201_2440669_+	pfam06177, QueT, QueT transporter	NA|326aa|down_8|NZ_CP047856.1_2440720_2441698_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|316aa|down_9|NZ_CP047856.1_2441699_2442647_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family
GCF_009912895.1_ASM991289v1	NZ_CP047856	Staphylococcus aureus strain UP_1435 chromosome, complete genome	7	2595603-2595683	6	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	CAAGTTGGCGGGGCCCCAACACAGA	25	1	15	2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658|2595628-2595658	NZ_CP047856.1_1235724-1235754|NZ_CP047856.1_1235780-1235810|NZ_CP047856.1_396400-396370|NZ_CP047856.1_681054-681024|NZ_CP047856.1_887153-887123|NZ_CP047856.1_1416432-1416402|NZ_CP047856.1_1683703-1683673|NZ_CP047856.1_80559-80589|NZ_CP047856.1_592476-592506|NZ_CP047856.1_592592-592622|NZ_CP047856.1_989452-989482|NZ_CP047856.1_1199450-1199480|NZ_CP047856.1_1235668-1235698|NZ_CP047856.1_2026723-2026753|NZ_CP047856.1_2606429-2606459	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|62aa|down_0|NZ_CP047856.1_2595724_2595910_-,NA|84aa|down_5|NZ_CP047856.1_2599049_2599301_-,NA|106aa|down_8|NZ_CP047856.1_2604422_2604740_-,NA|55aa|down_9|NZ_CP047856.1_2604984_2605149_-	NA|202aa|up_9|NZ_CP047856.1_2588495_2589101_+	COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]	NA|335aa|up_8|NZ_CP047856.1_2589270_2590275_+	PRK07688, PRK07688, thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated	NA|169aa|up_7|NZ_CP047856.1_2590305_2590812_+	COG0521, MoaB, Molybdopterin biosynthesis enzymes [Coenzyme metabolism]	NA|165aa|up_6|NZ_CP047856.1_2590813_2591308_-	PRK09364, moaC, cyclic pyranopterin monophosphate synthase MoaC	NA|420aa|up_5|NZ_CP047856.1_2591370_2592630_+	cd00887, MoeA, MoeA family	NA|162aa|up_4|NZ_CP047856.1_2592626_2593112_+	COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]	NA|149aa|up_3|NZ_CP047856.1_2593125_2593572_+	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism]	NA|78aa|up_2|NZ_CP047856.1_2593577_2593811_+	cd00754, Ubl_MoaD, ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins	NA|200aa|up_1|NZ_CP047856.1_2593817_2594417_+	PRK00317, mobA, molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed	NA|341aa|up_0|NZ_CP047856.1_2594436_2595459_+	TIGR02666, Cyclic_pyranopterin_monophosphate_synthase, molybdenum cofactor biosynthesis protein A, bacterial	NA|62aa|down_0|NZ_CP047856.1_2595724_2595910_-	NA	NA|117aa|down_1|NZ_CP047856.1_2596035_2596386_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|404aa|down_2|NZ_CP047856.1_2596487_2597699_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|147aa|down_3|NZ_CP047856.1_2597691_2598132_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|255aa|down_4|NZ_CP047856.1_2598293_2599058_+	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|84aa|down_5|NZ_CP047856.1_2599049_2599301_-	NA	NA|422aa|down_6|NZ_CP047856.1_2599689_2600955_+	COG2348, COG2348, Peptidoglycan interpeptide bridge formation enzyme [Cell wall/membrane/envelope biogenesis]	NA|1056aa|down_7|NZ_CP047856.1_2601071_2604239_+	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms]	NA|106aa|down_8|NZ_CP047856.1_2604422_2604740_-	NA	NA|55aa|down_9|NZ_CP047856.1_2604984_2605149_-	NA
GCF_009912895.1_ASM991289v1	NZ_CP047856	Staphylococcus aureus strain UP_1435 chromosome, complete genome	8	2705158-2705243	7	CRISPRCasFinder	no	csa3	DEDDh,csa3,cas3,DinG,WYL,RT	Type I-A	ACTAATGATACGCAAAAATCAGTTGG	26	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|53aa|down_7|NZ_CP047856.1_2716205_2716364_-,NA|35aa|down_8|NZ_CP047856.1_2717043_2717148_+,NA|364aa|down_9|NZ_CP047856.1_2717580_2718672_-	NA|228aa|up_9|NZ_CP047856.1_2680088_2680772_+	COG1272, COG1272, Predicted membrane protein, hemolysin III homolog [General function prediction only]	NA|448aa|up_8|NZ_CP047856.1_2680948_2682292_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|158aa|up_7|NZ_CP047856.1_2682390_2682864_+	pfam17080, SepA, Multidrug Resistance efflux pump	NA|481aa|up_6|NZ_CP047856.1_2683186_2684629_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|355aa|up_5|NZ_CP047856.1_2684776_2685841_+	pfam10609, ParA, NUBPL iron-transfer P-loop NTPase	NA|440aa|up_4|NZ_CP047856.1_2692131_2693451_+	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|303aa|up_3|NZ_CP047856.1_2693601_2694510_+	cd09989, Arginase, Arginase family	NA|270aa|up_2|NZ_CP047856.1_2694698_2695508_+	COG1624, COG1624, Uncharacterized conserved protein [Function unknown]	NA|311aa|up_1|NZ_CP047856.1_2695509_2696442_+	COG4856, COG4856, Uncharacterized protein conserved in bacteria [Function unknown]	NA|452aa|up_0|NZ_CP047856.1_2696468_2697824_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|369aa|down_0|NZ_CP047856.1_2705865_2706972_-	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|145aa|down_1|NZ_CP047856.1_2706971_2707406_-	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|711aa|down_2|NZ_CP047856.1_2707417_2709550_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|513aa|down_3|NZ_CP047856.1_2709584_2711123_-	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|602aa|down_4|NZ_CP047856.1_2711803_2713609_+	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|261aa|down_5|NZ_CP047856.1_2713840_2714623_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|down_6|NZ_CP047856.1_2714690_2715548_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|53aa|down_7|NZ_CP047856.1_2716205_2716364_-	NA	NA|35aa|down_8|NZ_CP047856.1_2717043_2717148_+	NA	NA|364aa|down_9|NZ_CP047856.1_2717580_2718672_-	NA
GCF_009912895.1_ASM991289v1	NZ_CP047856	Staphylococcus aureus strain UP_1435 chromosome, complete genome	9	2717483-2717564	8	CRISPRCasFinder	no	csa3	DEDDh,csa3,cas3,DinG,WYL,RT	Type I-A	AAGAAGCCCCTAACAACTAAAGTTG	25	0	0	NA	NA	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|53aa|up_1|NZ_CP047856.1_2716205_2716364_-,NA|35aa|up_0|NZ_CP047856.1_2717043_2717148_+,NA|364aa|down_0|NZ_CP047856.1_2717580_2718672_-,NA|77aa|down_5|NZ_CP047856.1_2722458_2722689_+	NA|2482aa|up_9|NZ_CP047856.1_2698101_2705547_+	TIGR04263, cell_wall_surface_anchor_family_protein, SasC/Mrp/FmtB intercellular aggregation domain	NA|369aa|up_8|NZ_CP047856.1_2705865_2706972_-	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|145aa|up_7|NZ_CP047856.1_2706971_2707406_-	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|711aa|up_6|NZ_CP047856.1_2707417_2709550_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|513aa|up_5|NZ_CP047856.1_2709584_2711123_-	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|602aa|up_4|NZ_CP047856.1_2711803_2713609_+	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|261aa|up_3|NZ_CP047856.1_2713840_2714623_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|up_2|NZ_CP047856.1_2714690_2715548_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|53aa|up_1|NZ_CP047856.1_2716205_2716364_-	NA	NA|35aa|up_0|NZ_CP047856.1_2717043_2717148_+	NA	NA|364aa|down_0|NZ_CP047856.1_2717580_2718672_-	NA	NA|326aa|down_1|NZ_CP047856.1_2718937_2719915_-	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	csa3|107aa|down_2|NZ_CP047856.1_2719916_2720237_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|222aa|down_3|NZ_CP047856.1_2720388_2721054_+	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	NA|313aa|down_4|NZ_CP047856.1_2721489_2722428_+	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|77aa|down_5|NZ_CP047856.1_2722458_2722689_+	NA	NA|458aa|down_6|NZ_CP047856.1_2723360_2724734_+	pfam01878, EVE, EVE domain	NA|138aa|down_7|NZ_CP047856.1_2725190_2725604_+	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|148aa|down_8|NZ_CP047856.1_2725803_2726247_+	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|237aa|down_9|NZ_CP047856.1_2726367_2727078_-	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase
GCF_009912895.1_ASM991289v1	NZ_CP047856	Staphylococcus aureus strain UP_1435 chromosome, complete genome	10	2846739-2846820	9	CRISPRCasFinder	no	DEDDh	DEDDh,csa3,cas3,DinG,WYL,RT	Unclear	ACAATGCAAGTTGGGGTGGGGGCC	24	1	5	2846763-2846796|2846763-2846796|2846763-2846796|2846763-2846796|2846763-2846796	NZ_CP047856.1_892754-892721|NZ_CP047856.1_1248521-1248554|NZ_CP047856.1_284329-284296|NZ_CP047856.1_676606-676639|NZ_CP047856.1_2157171-2157204	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|81aa|down_4|NZ_CP047856.1_2853011_2853254_-,NA|61aa|down_6|NZ_CP047856.1_2854347_2854530_-,NA|114aa|down_7|NZ_CP047856.1_2854733_2855075_-	NA|48aa|up_9|NZ_CP047856.1_2836923_2837067_-	smart00794, AgrD, Staphylococcal AgrD protein	NA|188aa|up_8|NZ_CP047856.1_2837069_2837633_-	COG4512, AgrB, Membrane protein putatively involved in post-translational modification of the autoinducing quorum-sensing peptide [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Transcription]	NA|45aa|up_7|NZ_CP047856.1_2837868_2838003_+	PRK14752, PRK14752, delta-lysin family phenol-soluble modulin	NA|262aa|up_6|NZ_CP047856.1_2838602_2839388_-	cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases)	NA|209aa|up_5|NZ_CP047856.1_2839748_2840375_-	COG3560, FMR2, Predicted oxidoreductase related to nitroreductase [General function prediction only]	NA|420aa|up_4|NZ_CP047856.1_2840571_2841831_+	PRK10819, PRK10819, transport protein TonB; Provisional	NA|248aa|up_3|NZ_CP047856.1_2841855_2842599_-	pfam02517, Abi, CAAX protease self-immunity	NA|95aa|up_2|NZ_CP047856.1_2842773_2843058_+	PRK00364, groES, co-chaperonin GroES; Reviewed	NA|539aa|up_1|NZ_CP047856.1_2843133_2844750_+	PRK00013, groEL, chaperonin GroEL; Reviewed	NA|436aa|up_0|NZ_CP047856.1_2845289_2846597_-	TIGR00933, Trk_system_potassium_uptake_protein_trkH	NA|408aa|down_0|NZ_CP047856.1_2847040_2848264_-	PRK08588, PRK08588, succinyl-diaminopimelate desuccinylase; Reviewed	NA|352aa|down_1|NZ_CP047856.1_2848699_2849755_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|339aa|down_2|NZ_CP047856.1_2849776_2850793_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|346aa|down_3|NZ_CP047856.1_2851911_2852949_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|81aa|down_4|NZ_CP047856.1_2853011_2853254_-	NA	NA|328aa|down_5|NZ_CP047856.1_2853264_2854248_-	pfam00535, Glycos_transf_2, Glycosyl transferase family 2	NA|61aa|down_6|NZ_CP047856.1_2854347_2854530_-	NA	NA|114aa|down_7|NZ_CP047856.1_2854733_2855075_-	NA	DEDDh|311aa|down_8|NZ_CP047856.1_2855080_2856013_-	PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated	NA|238aa|down_9|NZ_CP047856.1_2856028_2856742_-	COG2932, COG2932, Predicted transcriptional regulator [Transcription]
