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_009913175.1_ASM991317v1	NZ_CP047863	Staphylococcus aureus strain UP_1106 chromosome, complete genome	1	410982-411066	1	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TTCTACAGGCAATGCAAGTTGGGGTG	26	1	2	411008-411040|411008-411040	NZ_CP047863.1_681014-680982|NZ_CP047863.1_1243228-1243260	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA	NA|190aa|up_9|NZ_CP047863.1_401611_402181_+	TIGR00482, Probable_nicotinate-nucleotide_adenylyltransferase, nicotinate (nicotinamide) nucleotide adenylyltransferase	NA|195aa|up_8|NZ_CP047863.1_402170_402755_+	COG1713, COG1713, Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism]	NA|118aa|up_7|NZ_CP047863.1_402755_403109_+	COG0799, COG0799, Uncharacterized homolog of plant Iojap protein [Function unknown]	NA|239aa|up_6|NZ_CP047863.1_403111_403828_+	pfam13649, Methyltransf_25, Methyltransferase domain	NA|229aa|up_5|NZ_CP047863.1_403867_404554_+	COG1555, ComEA, DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]	NA|154aa|up_4|NZ_CP047863.1_404645_405107_+	TIGR02571, putative_dCMP_deaminase, ComE operon protein 2	NA|716aa|up_3|NZ_CP047863.1_405165_407313_+	COG2333, ComEC, Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]	NA|325aa|up_2|NZ_CP047863.1_407369_408344_+	PRK05574, holA, DNA polymerase III subunit delta; Reviewed	NA|84aa|up_1|NZ_CP047863.1_408388_408640_-	PRK00239, rpsT, 30S ribosomal protein S20; Reviewed	NA|608aa|up_0|NZ_CP047863.1_408985_410809_+	PRK05433, PRK05433, GTP-binding protein LepA; Provisional	NA|375aa|down_0|NZ_CP047863.1_411374_412499_+	PRK08599, PRK08599, oxygen-independent coproporphyrinogen III oxidase	NA|326aa|down_1|NZ_CP047863.1_412599_413577_+	TIGR00331, Heat-inducible_transcription_repressor_HrcA, heat shock gene repressor HrcA	NA|209aa|down_2|NZ_CP047863.1_413608_414235_+	PRK14140, PRK14140, heat shock protein GrpE; Provisional	NA|611aa|down_3|NZ_CP047863.1_414303_416136_+	PRK00290, dnaK, molecular chaperone DnaK; Provisional	NA|380aa|down_4|NZ_CP047863.1_416271_417411_+	PRK14280, PRK14280, molecular chaperone DnaJ	NA|313aa|down_5|NZ_CP047863.1_417414_418353_+	pfam06325, PrmA, Ribosomal protein L11 methyltransferase (PrmA)	NA|251aa|down_6|NZ_CP047863.1_418354_419107_+	COG1385, COG1385, Uncharacterized protein conserved in bacteria [Function unknown]	NA|449aa|down_7|NZ_CP047863.1_419113_420460_+	COG0621, MiaB, 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]	NA|59aa|down_8|NZ_CP047863.1_420752_420929_+	PRK00270, rpsU, 30S ribosomal protein S21; Reviewed	NA|228aa|down_9|NZ_CP047863.1_421172_421856_+	COG1030, NfeD, Membrane-bound serine protease (ClpP class) [Posttranslational modification, protein turnover, chaperones]
GCF_009913175.1_ASM991317v1	NZ_CP047863	Staphylococcus aureus strain UP_1106 chromosome, complete genome	2	1199999-1200080	2	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TTCTACAGGCAATGCAAGTTGGGG	24	1	1	1200023-1200056	NZ_CP047863.1_681015-680982	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|38aa|down_1|NZ_CP047863.1_1201063_1201177_-	NA|414aa|up_9|NZ_CP047863.1_1190426_1191668_-	TIGR01979, Probable_cysteine_desulfurase, cysteine desulfurases, SufSfamily	NA|436aa|up_8|NZ_CP047863.1_1191782_1193090_-	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]	NA|254aa|up_7|NZ_CP047863.1_1193187_1193949_-	COG0396, sufC, Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]	NA|284aa|up_6|NZ_CP047863.1_1194276_1195128_+	COG2035, COG2035, Predicted membrane protein [Function unknown]	NA|65aa|up_5|NZ_CP047863.1_1195361_1195556_-	COG3237, COG3237, Uncharacterized protein conserved in bacteria [Function unknown]	NA|274aa|up_4|NZ_CP047863.1_1195909_1196731_-	COG1464, NlpA, ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]	NA|232aa|up_3|NZ_CP047863.1_1196748_1197444_-	COG2011, AbcD, ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]	NA|342aa|up_2|NZ_CP047863.1_1197436_1198462_-	COG1135, AbcC, ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]	NA|99aa|up_1|NZ_CP047863.1_1198711_1199008_-	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_CP047863.1_1199000_1199387_-	COG1658, COG1658, Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]	NA|293aa|down_0|NZ_CP047863.1_1200183_1201062_-	COG3878, COG3878, Uncharacterized protein conserved in bacteria [Function unknown]	NA|38aa|down_1|NZ_CP047863.1_1201063_1201177_-	NA	NA|127aa|down_2|NZ_CP047863.1_1201240_1201621_-	PRK01202, PRK01202, glycine cleavage system protein GcvH	NA|119aa|down_3|NZ_CP047863.1_1201778_1202135_-	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_CP047863.1_1202278_1202599_+	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_CP047863.1_1202749_1203289_-	cd02135, YdjA-like, nitroreductase family protein similar to Escherichia coli YdjA	NA|239aa|down_6|NZ_CP047863.1_1203371_1204088_-	PRK13575, PRK13575, type I 3-dehydroquinate dehydratase	NA|141aa|down_7|NZ_CP047863.1_1204235_1204658_+	TIGR03561, organ_hyd_perox, peroxiredoxin, Ohr subfamily	NA|165aa|down_8|NZ_CP047863.1_1205056_1205551_+	pfam13420, Acetyltransf_4, Acetyltransferase (GNAT) domain	NA|206aa|down_9|NZ_CP047863.1_1205705_1206323_+	COG1279, COG1279, Lysine efflux permease [General function prediction only]
GCF_009913175.1_ASM991317v1	NZ_CP047863	Staphylococcus aureus strain UP_1106 chromosome, complete genome	3	1248739-1248817	3	CRISPRCasFinder	no	cas3	DEDDh,csa3,cas3,DinG,WYL,RT	Unclear	AGAATTTCGAAAAGAAATTCTACA	24	1	3	1248763-1248793|1248763-1248793|1248763-1248793	NZ_CP047863.1_1755096-1755066|NZ_CP047863.1_376554-376584|NZ_CP047863.1_1755151-1755121	NA	1	1	Unclear	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|36aa|down_5|NZ_CP047863.1_1256295_1256403_-,NA|35aa|down_7|NZ_CP047863.1_1257835_1257940_-	NA|301aa|up_9|NZ_CP047863.1_1237621_1238524_+	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|196aa|up_8|NZ_CP047863.1_1238766_1239354_-	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|315aa|up_7|NZ_CP047863.1_1239917_1240862_-	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|332aa|up_6|NZ_CP047863.1_1240972_1241968_-	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|304aa|up_5|NZ_CP047863.1_1241964_1242876_-	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|312aa|up_4|NZ_CP047863.1_1243760_1244696_-	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|480aa|up_3|NZ_CP047863.1_1244762_1246202_-	sd00008, TPR_YbbN, C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs	NA|162aa|up_2|NZ_CP047863.1_1246209_1246695_-	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_CP047863.1_1246702_1247542_-	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|311aa|up_0|NZ_CP047863.1_1247547_1248480_-	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|949aa|down_0|NZ_CP047863.1_1249143_1251990_-	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|662aa|down_1|NZ_CP047863.1_1251997_1253983_-	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|79aa|down_2|NZ_CP047863.1_1254251_1254488_-	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|217aa|down_3|NZ_CP047863.1_1254484_1255135_-	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|280aa|down_4|NZ_CP047863.1_1255308_1256148_-	COG3942, COG3942, Surface antigen [General function prediction only]	NA|36aa|down_5|NZ_CP047863.1_1256295_1256403_-	NA	NA|370aa|down_6|NZ_CP047863.1_1256556_1257667_-	PRK00578, prfB, peptide chain release factor 2; Validated	NA|35aa|down_7|NZ_CP047863.1_1257835_1257940_-	NA	NA|844aa|down_8|NZ_CP047863.1_1257981_1260513_-	PRK12904, PRK12904, preprotein translocase subunit SecA; Reviewed	NA|191aa|down_9|NZ_CP047863.1_1260926_1261499_-	COG1544, COG1544, Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
GCF_009913175.1_ASM991317v1	NZ_CP047863	Staphylococcus aureus strain UP_1106 chromosome, complete genome	4	1639922-1640024	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_CP047863.1_1631540_1632077_+,NA|221aa|up_1|NZ_CP047863.1_1638168_1638831_+,NA|33aa|down_0|NZ_CP047863.1_1640699_1640798_-,NA|128aa|down_6|NZ_CP047863.1_1647045_1647429_+,NA|70aa|down_8|NZ_CP047863.1_1648253_1648463_+	NA|91aa|up_9|NZ_CP047863.1_1629773_1630046_+	COG2963, COG2963, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|235aa|up_8|NZ_CP047863.1_1630444_1631149_+	pfam02452, PemK_toxin, PemK-like, MazF-like toxin of type II toxin-antitoxin system	NA|179aa|up_7|NZ_CP047863.1_1631540_1632077_+	NA	NA|514aa|up_6|NZ_CP047863.1_1632189_1633731_-	PRK00074, guaA, GMP synthase; Reviewed	NA|489aa|up_5|NZ_CP047863.1_1633755_1635222_-	PRK05567, PRK05567, inosine 5'-monophosphate dehydrogenase; Reviewed	NA|423aa|up_4|NZ_CP047863.1_1635259_1636528_-	TIGR03173, pbuX, xanthine permease	NA|193aa|up_3|NZ_CP047863.1_1636527_1637106_-	PRK09219, PRK09219, xanthine phosphoribosyltransferase; Validated	NA|136aa|up_2|NZ_CP047863.1_1637618_1638026_+	pfam11181, YflT, Heat induced stress protein YflT	NA|221aa|up_1|NZ_CP047863.1_1638168_1638831_+	NA	NA|319aa|up_0|NZ_CP047863.1_1638948_1639905_+	TIGR02168, Chromosome_partition_protein_Smc, chromosome segregation protein SMC, common bacterial type	NA|33aa|down_0|NZ_CP047863.1_1640699_1640798_-	NA	NA|463aa|down_1|NZ_CP047863.1_1640882_1642271_+	COG1823, COG1823, Predicted Na+/dicarboxylate symporter [General function prediction only]	NA|252aa|down_2|NZ_CP047863.1_1642350_1643106_-	cd02146, NfsA-like, nitroreductase similar to Escherichia coli NfsA	NA|190aa|down_3|NZ_CP047863.1_1643597_1644167_+	TIGR03137, AhpC, peroxiredoxin	NA|508aa|down_4|NZ_CP047863.1_1644182_1645706_+	PRK15317, PRK15317, alkyl hydroperoxide reductase subunit F; Provisional	NA|209aa|down_5|NZ_CP047863.1_1646149_1646776_+	NF033193, lipo_NDxxF, NDxxF motif lipoprotein	NA|128aa|down_6|NZ_CP047863.1_1647045_1647429_+	NA	NA|194aa|down_7|NZ_CP047863.1_1647494_1648076_-	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|70aa|down_8|NZ_CP047863.1_1648253_1648463_+	NA	NA|84aa|down_9|NZ_CP047863.1_1648501_1648753_-	COG2261, COG2261, Predicted membrane protein [Function unknown]
GCF_009913175.1_ASM991317v1	NZ_CP047863	Staphylococcus aureus strain UP_1106 chromosome, complete genome	5	2304857-2304990	1	PILER-CR	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TATTGAAGAAGATACAA	17	2	2	2304874-2304919|2304937-2304973	NZ_CP047863.1_2301350-2301395|NZ_CP047863.1_2301413-2301449	NA	2	2	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|67aa|up_1|NZ_CP047863.1_2298526_2298727_+,NA|78aa|down_5|NZ_CP047863.1_2313307_2313541_+,NA|103aa|down_6|NZ_CP047863.1_2313648_2313957_-,NA|89aa|down_7|NZ_CP047863.1_2314100_2314367_-	NA|426aa|up_9|NZ_CP047863.1_2288523_2289801_+	cd17319, MFS_ExuT_GudP_like, Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily	NA|608aa|up_8|NZ_CP047863.1_2290277_2292101_+	COG1289, COG1289, Predicted membrane protein [Function unknown]	NA|139aa|up_7|NZ_CP047863.1_2292239_2292656_+	COG4876, COG4876, Uncharacterized protein conserved in bacteria [Function unknown]	NA|231aa|up_6|NZ_CP047863.1_2292886_2293579_+	COG2357, COG2357, PpGpp synthetase catalytic domain [General function prediction only]	NA|255aa|up_5|NZ_CP047863.1_2293743_2294508_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|227aa|up_4|NZ_CP047863.1_2294660_2295341_+	COG1802, GntR, Transcriptional regulators [Transcription]	NA|518aa|up_3|NZ_CP047863.1_2295364_2296918_+	TIGR01314, gntK_FGGY, gluconate kinase, FGGY type	NA|453aa|up_2|NZ_CP047863.1_2297034_2298393_+	TIGR00791, Gluconate_permease, gluconate transporter	NA|67aa|up_1|NZ_CP047863.1_2298526_2298727_+	NA	NA|997aa|up_0|NZ_CP047863.1_2298861_2301852_+	pfam10425, SdrG_C_C, C-terminus of bacterial fibrinogen-binding adhesin	NA|289aa|down_0|NZ_CP047863.1_2305598_2306465_+	COG1210, GalU, UDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]	NA|248aa|down_1|NZ_CP047863.1_2306675_2307419_-	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|119aa|down_2|NZ_CP047863.1_2307742_2308099_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|1116aa|down_3|NZ_CP047863.1_2308403_2311751_+	pfam18483, Bact_lectin, Bacterial lectin	NA|359aa|down_4|NZ_CP047863.1_2312134_2313211_+	cd06173, MFS_MefA_like, Macrolide efflux protein A and similar proteins of the Major Facilitator Superfamily of transporters	NA|78aa|down_5|NZ_CP047863.1_2313307_2313541_+	NA	NA|103aa|down_6|NZ_CP047863.1_2313648_2313957_-	NA	NA|89aa|down_7|NZ_CP047863.1_2314100_2314367_-	NA	NA|603aa|down_8|NZ_CP047863.1_2314650_2316459_-	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|131aa|down_9|NZ_CP047863.1_2316590_2316983_+	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_009913175.1_ASM991317v1	NZ_CP047863	Staphylococcus aureus strain UP_1106 chromosome, complete genome	6	2380404-2380482	5	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	TGCAAGTTGGCGGGGCCCCAACA	23	1	5	2380427-2380459|2380427-2380459|2380427-2380459|2380427-2380459|2380427-2380459	NZ_CP047863.1_1199710-1199742|NZ_CP047863.1_1235929-1235961|NZ_CP047863.1_2772341-2772309|NZ_CP047863.1_1235985-1236017|NZ_CP047863.1_1236041-1236073	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA|220aa|up_3|NZ_CP047863.1_2377328_2377988_-,NA|36aa|up_0|NZ_CP047863.1_2379977_2380085_+,NA	NA|693aa|up_9|NZ_CP047863.1_2369790_2371869_-	COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic ion transport and metabolism]	NA|470aa|up_8|NZ_CP047863.1_2372006_2373416_-	COG1113, AnsP, Gamma-aminobutyrate permease and related permeases [Amino acid transport and metabolism]	NA|269aa|up_7|NZ_CP047863.1_2373701_2374508_+	TIGR03729, acc_ester, putative phosphoesterase	NA|219aa|up_6|NZ_CP047863.1_2374570_2375227_-	COG4990, COG4990, Uncharacterized protein conserved in bacteria [Function unknown]	NA|158aa|up_5|NZ_CP047863.1_2375339_2375813_+	COG3708, COG3708, Uncharacterized protein conserved in bacteria [Function unknown]	NA|404aa|up_4|NZ_CP047863.1_2375935_2377147_-	cd17320, MFS_MdfA_MDR_like, Multidrug transporter MdfA and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|220aa|up_3|NZ_CP047863.1_2377328_2377988_-	NA	NA|381aa|up_2|NZ_CP047863.1_2378047_2379190_-	TIGR00045, Glycerate_kinase, glycerate kinase	NA|129aa|up_1|NZ_CP047863.1_2379457_2379844_+	COG2246, COG2246, Predicted membrane protein [Function unknown]	NA|36aa|up_0|NZ_CP047863.1_2379977_2380085_+	NA	NA|588aa|down_0|NZ_CP047863.1_2380787_2382551_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|578aa|down_1|NZ_CP047863.1_2382575_2384309_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|229aa|down_2|NZ_CP047863.1_2384761_2385448_+	COG0132, BioD, Dethiobiotin synthetase [Coenzyme metabolism]	NA|453aa|down_3|NZ_CP047863.1_2385425_2386784_+	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase	NA|336aa|down_4|NZ_CP047863.1_2386785_2387793_+	PRK06256, PRK06256, biotin synthase; Validated	NA|372aa|down_5|NZ_CP047863.1_2387770_2388886_+	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|231aa|down_6|NZ_CP047863.1_2388896_2389589_+	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|156aa|down_7|NZ_CP047863.1_2389599_2390067_+	pfam06177, QueT, QueT transporter	NA|326aa|down_8|NZ_CP047863.1_2390118_2391096_-	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|316aa|down_9|NZ_CP047863.1_2391097_2392045_-	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family
GCF_009913175.1_ASM991317v1	NZ_CP047863	Staphylococcus aureus strain UP_1106 chromosome, complete genome	7	2545192-2545272	6	CRISPRCasFinder	no		DEDDh,csa3,cas3,DinG,WYL,RT	Orphan	CAAGTTGGCGGGGCCCCAACACAGA	25	1	15	2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247|2545217-2545247	NZ_CP047863.1_1235989-1236019|NZ_CP047863.1_1236045-1236075|NZ_CP047863.1_396402-396372|NZ_CP047863.1_681056-681026|NZ_CP047863.1_887156-887126|NZ_CP047863.1_1416704-1416674|NZ_CP047863.1_1678761-1678731|NZ_CP047863.1_80559-80589|NZ_CP047863.1_592478-592508|NZ_CP047863.1_592594-592624|NZ_CP047863.1_989717-989747|NZ_CP047863.1_1199714-1199744|NZ_CP047863.1_1235933-1235963|NZ_CP047863.1_1976920-1976950|NZ_CP047863.1_2556018-2556048	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|62aa|down_0|NZ_CP047863.1_2545313_2545499_-,NA|84aa|down_5|NZ_CP047863.1_2548638_2548890_-,NA|106aa|down_8|NZ_CP047863.1_2554011_2554329_-,NA|55aa|down_9|NZ_CP047863.1_2554573_2554738_-	NA|202aa|up_9|NZ_CP047863.1_2538084_2538690_+	COG4148, ModC, ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]	NA|335aa|up_8|NZ_CP047863.1_2538859_2539864_+	PRK07688, PRK07688, thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated	NA|169aa|up_7|NZ_CP047863.1_2539894_2540401_+	COG0521, MoaB, Molybdopterin biosynthesis enzymes [Coenzyme metabolism]	NA|165aa|up_6|NZ_CP047863.1_2540402_2540897_-	PRK09364, moaC, cyclic pyranopterin monophosphate synthase MoaC	NA|420aa|up_5|NZ_CP047863.1_2540959_2542219_+	cd00887, MoeA, MoeA family	NA|162aa|up_4|NZ_CP047863.1_2542215_2542701_+	COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]	NA|149aa|up_3|NZ_CP047863.1_2542714_2543161_+	COG0314, MoaE, Molybdopterin converting factor, large subunit [Coenzyme metabolism]	NA|78aa|up_2|NZ_CP047863.1_2543166_2543400_+	cd00754, Ubl_MoaD, ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins	NA|200aa|up_1|NZ_CP047863.1_2543406_2544006_+	PRK00317, mobA, molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed	NA|341aa|up_0|NZ_CP047863.1_2544025_2545048_+	TIGR02666, Cyclic_pyranopterin_monophosphate_synthase, molybdenum cofactor biosynthesis protein A, bacterial	NA|62aa|down_0|NZ_CP047863.1_2545313_2545499_-	NA	NA|117aa|down_1|NZ_CP047863.1_2545624_2545975_+	TIGR01889, Pleiotropic_Regulator_Of_Virulence, staphylococcal accessory regulator family	NA|404aa|down_2|NZ_CP047863.1_2546076_2547288_-	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily	NA|147aa|down_3|NZ_CP047863.1_2547280_2547721_-	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|255aa|down_4|NZ_CP047863.1_2547882_2548647_+	pfam13468, Glyoxalase_3, Glyoxalase-like domain	NA|84aa|down_5|NZ_CP047863.1_2548638_2548890_-	NA	NA|422aa|down_6|NZ_CP047863.1_2549278_2550544_+	COG2348, COG2348, Peptidoglycan interpeptide bridge formation enzyme [Cell wall/membrane/envelope biogenesis]	NA|1056aa|down_7|NZ_CP047863.1_2550660_2553828_+	COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms]	NA|106aa|down_8|NZ_CP047863.1_2554011_2554329_-	NA	NA|55aa|down_9|NZ_CP047863.1_2554573_2554738_-	NA
GCF_009913175.1_ASM991317v1	NZ_CP047863	Staphylococcus aureus strain UP_1106 chromosome, complete genome	8	2654746-2654831	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_CP047863.1_2665793_2665952_-,NA|35aa|down_8|NZ_CP047863.1_2666631_2666736_+,NA|364aa|down_9|NZ_CP047863.1_2667168_2668260_-	NA|228aa|up_9|NZ_CP047863.1_2629676_2630360_+	COG1272, COG1272, Predicted membrane protein, hemolysin III homolog [General function prediction only]	NA|448aa|up_8|NZ_CP047863.1_2630536_2631880_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|158aa|up_7|NZ_CP047863.1_2631978_2632452_+	pfam17080, SepA, Multidrug Resistance efflux pump	NA|481aa|up_6|NZ_CP047863.1_2632774_2634217_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|355aa|up_5|NZ_CP047863.1_2634364_2635429_+	pfam10609, ParA, NUBPL iron-transfer P-loop NTPase	NA|440aa|up_4|NZ_CP047863.1_2641719_2643039_+	COG3464, COG3464, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|303aa|up_3|NZ_CP047863.1_2643189_2644098_+	cd09989, Arginase, Arginase family	NA|270aa|up_2|NZ_CP047863.1_2644286_2645096_+	COG1624, COG1624, Uncharacterized conserved protein [Function unknown]	NA|311aa|up_1|NZ_CP047863.1_2645097_2646030_+	COG4856, COG4856, Uncharacterized protein conserved in bacteria [Function unknown]	NA|452aa|up_0|NZ_CP047863.1_2646056_2647412_+	PRK14316, glmM, phosphoglucosamine mutase; Provisional	NA|369aa|down_0|NZ_CP047863.1_2655453_2656560_-	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|145aa|down_1|NZ_CP047863.1_2656559_2656994_-	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|711aa|down_2|NZ_CP047863.1_2657005_2659138_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|513aa|down_3|NZ_CP047863.1_2659172_2660711_-	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|602aa|down_4|NZ_CP047863.1_2661391_2663197_+	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|261aa|down_5|NZ_CP047863.1_2663428_2664211_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|down_6|NZ_CP047863.1_2664278_2665136_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|53aa|down_7|NZ_CP047863.1_2665793_2665952_-	NA	NA|35aa|down_8|NZ_CP047863.1_2666631_2666736_+	NA	NA|364aa|down_9|NZ_CP047863.1_2667168_2668260_-	NA
GCF_009913175.1_ASM991317v1	NZ_CP047863	Staphylococcus aureus strain UP_1106 chromosome, complete genome	9	2667071-2667152	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_CP047863.1_2665793_2665952_-,NA|35aa|up_0|NZ_CP047863.1_2666631_2666736_+,NA|364aa|down_0|NZ_CP047863.1_2667168_2668260_-,NA|77aa|down_5|NZ_CP047863.1_2672046_2672277_+	NA|2482aa|up_9|NZ_CP047863.1_2647689_2655135_+	TIGR04263, cell_wall_surface_anchor_family_protein, SasC/Mrp/FmtB intercellular aggregation domain	NA|369aa|up_8|NZ_CP047863.1_2655453_2656560_-	PRK02318, PRK02318, mannitol-1-phosphate 5-dehydrogenase; Provisional	NA|145aa|up_7|NZ_CP047863.1_2656559_2656994_-	COG4668, MtlA, Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]	NA|711aa|up_6|NZ_CP047863.1_2657005_2659138_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|513aa|up_5|NZ_CP047863.1_2659172_2660711_-	COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]	NA|602aa|up_4|NZ_CP047863.1_2661391_2663197_+	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|261aa|up_3|NZ_CP047863.1_2663428_2664211_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|286aa|up_2|NZ_CP047863.1_2664278_2665136_+	COG0561, Cof, Predicted hydrolases of the HAD superfamily [General function prediction only]	NA|53aa|up_1|NZ_CP047863.1_2665793_2665952_-	NA	NA|35aa|up_0|NZ_CP047863.1_2666631_2666736_+	NA	NA|364aa|down_0|NZ_CP047863.1_2667168_2668260_-	NA	NA|326aa|down_1|NZ_CP047863.1_2668525_2669503_-	COG1230, CzcD, Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]	csa3|107aa|down_2|NZ_CP047863.1_2669504_2669825_-	cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors	NA|222aa|down_3|NZ_CP047863.1_2669976_2670642_+	cd05243, SDR_a5, atypical (a) SDRs, subgroup 5	NA|313aa|down_4|NZ_CP047863.1_2671077_2672016_+	COG1482, ManA, Phosphomannose isomerase [Carbohydrate transport and metabolism]	NA|77aa|down_5|NZ_CP047863.1_2672046_2672277_+	NA	NA|458aa|down_6|NZ_CP047863.1_2672948_2674322_+	pfam01878, EVE, EVE domain	NA|138aa|down_7|NZ_CP047863.1_2674778_2675192_+	COG3011, COG3011, Predicted thiol-disulfide oxidoreductase [General function    prediction only]	NA|148aa|down_8|NZ_CP047863.1_2675391_2675835_+	COG0783, Dps, DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]	NA|237aa|down_9|NZ_CP047863.1_2675955_2676666_-	PRK05819, deoD, DeoD-type purine-nucleoside phosphorylase
GCF_009913175.1_ASM991317v1	NZ_CP047863	Staphylococcus aureus strain UP_1106 chromosome, complete genome	10	2796327-2796408	9	CRISPRCasFinder	no	DEDDh	DEDDh,csa3,cas3,DinG,WYL,RT	Unclear	ACAATGCAAGTTGGGGTGGGGGCC	24	1	5	2796351-2796384|2796351-2796384|2796351-2796384|2796351-2796384|2796351-2796384	NZ_CP047863.1_892757-892724|NZ_CP047863.1_1248785-1248818|NZ_CP047863.1_284330-284297|NZ_CP047863.1_676608-676641|NZ_CP047863.1_2106570-2106603	NA	1	1	Orphan	DEDDh,csa3,cas3,DinG,WYL,RT	NA,NA|81aa|down_4|NZ_CP047863.1_2802599_2802842_-,NA|61aa|down_6|NZ_CP047863.1_2803935_2804118_-,NA|114aa|down_7|NZ_CP047863.1_2804321_2804663_-	NA|48aa|up_9|NZ_CP047863.1_2786511_2786655_-	smart00794, AgrD, Staphylococcal AgrD protein	NA|188aa|up_8|NZ_CP047863.1_2786657_2787221_-	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_CP047863.1_2787456_2787591_+	PRK14752, PRK14752, delta-lysin family phenol-soluble modulin	NA|262aa|up_6|NZ_CP047863.1_2788190_2788976_-	cd07583, nitrilase_5, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases)	NA|209aa|up_5|NZ_CP047863.1_2789336_2789963_-	COG3560, FMR2, Predicted oxidoreductase related to nitroreductase [General function prediction only]	NA|420aa|up_4|NZ_CP047863.1_2790159_2791419_+	PRK10819, PRK10819, transport protein TonB; Provisional	NA|248aa|up_3|NZ_CP047863.1_2791443_2792187_-	pfam02517, Abi, CAAX protease self-immunity	NA|95aa|up_2|NZ_CP047863.1_2792361_2792646_+	PRK00364, groES, co-chaperonin GroES; Reviewed	NA|539aa|up_1|NZ_CP047863.1_2792721_2794338_+	PRK00013, groEL, chaperonin GroEL; Reviewed	NA|436aa|up_0|NZ_CP047863.1_2794877_2796185_-	TIGR00933, Trk_system_potassium_uptake_protein_trkH	NA|408aa|down_0|NZ_CP047863.1_2796628_2797852_-	PRK08588, PRK08588, succinyl-diaminopimelate desuccinylase; Reviewed	NA|352aa|down_1|NZ_CP047863.1_2798287_2799343_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|339aa|down_2|NZ_CP047863.1_2799364_2800381_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|346aa|down_3|NZ_CP047863.1_2801499_2802537_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|81aa|down_4|NZ_CP047863.1_2802599_2802842_-	NA	NA|328aa|down_5|NZ_CP047863.1_2802852_2803836_-	pfam00535, Glycos_transf_2, Glycosyl transferase family 2	NA|61aa|down_6|NZ_CP047863.1_2803935_2804118_-	NA	NA|114aa|down_7|NZ_CP047863.1_2804321_2804663_-	NA	DEDDh|311aa|down_8|NZ_CP047863.1_2804668_2805601_-	PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated	NA|238aa|down_9|NZ_CP047863.1_2805616_2806330_-	COG2932, COG2932, Predicted transcriptional regulator [Transcription]
