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_009912455.1_ASM991245v1	NZ_CP047787	Staphylococcus aureus strain UP_1108 chromosome, complete genome	1	781697-781780	1	CRISPRCasFinder	no	cas3	cas3,DEDDh,DinG,csa3,WYL	Unclear	GTAAGCTGACTTTACGTTAGCTTCT	25	1	1	781722-781755	NZ_CP047787.1_1016166-1016199	NA	1	1	Unclear	cas3,DEDDh,DinG,csa3,WYL	NA,NA	NA|280aa|up_9|NZ_CP047787.1_769118_769958_+	COG3942, COG3942, Surface antigen [General function prediction only]	NA|217aa|up_8|NZ_CP047787.1_770131_770782_+	pfam12917, HD_2, HD containing hydrolase-like enzyme	NA|79aa|up_7|NZ_CP047787.1_770778_771015_+	COG4897, CsbA, Uncharacterized protein conserved in bacteria [Function unknown]	NA|662aa|up_6|NZ_CP047787.1_771283_773269_+	PRK05298, PRK05298, excinuclease ABC subunit UvrB	NA|943aa|up_5|NZ_CP047787.1_773276_776105_+	PRK00349, uvrA, excinuclease ABC subunit UvrA	NA|311aa|up_4|NZ_CP047787.1_776481_777414_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_3|NZ_CP047787.1_777419_778259_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_2|NZ_CP047787.1_778266_778752_+	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_CP047787.1_778759_780199_+	sd00006, TPR, Tetratricopeptide repeat	NA|312aa|up_0|NZ_CP047787.1_780265_781201_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|down_0|NZ_CP047787.1_782028_782940_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|down_1|NZ_CP047787.1_782936_783932_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|down_2|NZ_CP047787.1_784042_784987_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|down_3|NZ_CP047787.1_785549_786137_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|545aa|down_4|NZ_CP047787.1_786318_787953_+	PRK13529, PRK13529, oxaloacetate-decarboxylating malate dehydrogenase	NA|301aa|down_5|NZ_CP047787.1_788399_789302_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_6|NZ_CP047787.1_790004_790634_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_7|NZ_CP047787.1_791242_792256_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_8|NZ_CP047787.1_792308_793319_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_9|NZ_CP047787.1_793457_794648_+	PRK00073, pgk, phosphoglycerate kinase; Provisional
GCF_009912455.1_ASM991245v1	NZ_CP047787	Staphylococcus aureus strain UP_1108 chromosome, complete genome	2	788170-788249	2	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CAGCTTCTATGTTGGGGCCCCGCC	24	1	6	788194-788225|788194-788225|788194-788225|788194-788225|788194-788225|788194-788225	NZ_CP047787.1_228852-228821|NZ_CP047787.1_2234210-2234179|NZ_CP047787.1_2234266-2234235|NZ_CP047787.1_2234322-2234291|NZ_CP047787.1_2392836-2392805|NZ_CP047787.1_1837975-1837944	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA,NA|153aa|down_8|NZ_CP047787.1_798823_799282_+	NA|311aa|up_9|NZ_CP047787.1_776481_777414_+	PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional	NA|280aa|up_8|NZ_CP047787.1_777419_778259_+	PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase; Reviewed	NA|162aa|up_7|NZ_CP047787.1_778266_778752_+	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_6|NZ_CP047787.1_778759_780199_+	sd00006, TPR, Tetratricopeptide repeat	NA|312aa|up_5|NZ_CP047787.1_780265_781201_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|304aa|up_4|NZ_CP047787.1_782028_782940_+	COG1660, COG1660, Predicted P-loop-containing kinase [General function prediction only]	NA|332aa|up_3|NZ_CP047787.1_782936_783932_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|315aa|up_2|NZ_CP047787.1_784042_784987_+	TIGR00647, DNA_bind_WhiA, DNA-binding protein WhiA	NA|196aa|up_1|NZ_CP047787.1_785549_786137_+	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|545aa|up_0|NZ_CP047787.1_786318_787953_+	PRK13529, PRK13529, oxaloacetate-decarboxylating malate dehydrogenase	NA|301aa|down_0|NZ_CP047787.1_788399_789302_-	COG1090, COG1090, Predicted nucleoside-diphosphate sugar epimerase [General function prediction only]	NA|210aa|down_1|NZ_CP047787.1_790004_790634_+	PRK00409, PRK00409, recombination and DNA strand exchange inhibitor protein; Reviewed	NA|338aa|down_2|NZ_CP047787.1_791242_792256_+	COG2390, DeoR, Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]	NA|337aa|down_3|NZ_CP047787.1_792308_793319_+	TIGR01534, Glyceraldehyde-3-phosphate_dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, type I	NA|397aa|down_4|NZ_CP047787.1_793457_794648_+	PRK00073, pgk, phosphoglycerate kinase; Provisional	NA|254aa|down_5|NZ_CP047787.1_794769_795531_+	PRK00042, tpiA, triosephosphate isomerase; Provisional	NA|506aa|down_6|NZ_CP047787.1_795533_797051_+	PRK05434, PRK05434, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase	NA|435aa|down_7|NZ_CP047787.1_797180_798485_+	PRK00077, eno, enolase; Provisional	NA|153aa|down_8|NZ_CP047787.1_798823_799282_+	NA	NA|78aa|down_9|NZ_CP047787.1_799348_799582_+	COG1314, SecG, Preprotein translocase subunit SecG [Intracellular trafficking and secretion]
GCF_009912455.1_ASM991245v1	NZ_CP047787	Staphylococcus aureus strain UP_1108 chromosome, complete genome	3	876713-876880	1,3	PILER-CR,CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	CAAGTTGGCGGGGCCCCAACACAGAAGCTGGCGAAAAGCCAG,AAAGTCAGCTTACAATAATGTGCAAGTTGG	42,30	2	21	876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876830-876843|876825-876850|876825-876850|876825-876850|876825-876850	NZ_CP047787.1_228833-228846|NZ_CP047787.1_265986-265999|NZ_CP047787.1_781701-781688|NZ_CP047787.1_788157-788144|NZ_CP047787.1_828063-828050|NZ_CP047787.1_989836-989823|NZ_CP047787.1_1090282-1090295|NZ_CP047787.1_1309790-1309777|NZ_CP047787.1_2188782-2188769|NZ_CP047787.1_2199588-2199575|NZ_CP047787.1_2199702-2199689|NZ_CP047787.1_2234079-2234092|NZ_CP047787.1_2234135-2234148|NZ_CP047787.1_2234191-2234204|NZ_CP047787.1_2234247-2234260|NZ_CP047787.1_2234303-2234316|NZ_CP047787.1_2392817-2392830|NZ_CP047787.1_228799-228824|NZ_CP047787.1_2234157-2234182|NZ_CP047787.1_2234213-2234238|NZ_CP047787.1_2234269-2234294	NA:NA	2,1	2	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA,NA	NA|499aa|up_9|NZ_CP047787.1_865628_867125_-	PRK07691, PRK07691, putative monovalent cation/H+ antiporter subunit D; Reviewed	NA|110aa|up_8|NZ_CP047787.1_867117_867447_-	PRK08600, PRK08600, putative monovalent cation/H+ antiporter subunit C; Reviewed	NA|143aa|up_7|NZ_CP047787.1_867458_867887_-	PRK12573, PRK12573, Na(+)/H(+) antiporter subunit B	NA|802aa|up_6|NZ_CP047787.1_867879_870285_-	PRK12645, PRK12645, monovalent cation/H+ antiporter subunit A; Reviewed	NA|128aa|up_5|NZ_CP047787.1_870415_870799_-	pfam08810, KapB, Kinase associated protein B	NA|198aa|up_4|NZ_CP047787.1_870862_871456_+	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain	NA|126aa|up_3|NZ_CP047787.1_871871_872249_+	COG1098, VacB, Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]	NA|376aa|up_2|NZ_CP047787.1_872609_873737_+	cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN binding domain, group 4	NA|397aa|up_1|NZ_CP047787.1_874044_875235_+	PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional	NA|415aa|up_0|NZ_CP047787.1_875343_876588_+	COG0334, GdhA, Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]	NA|310aa|down_0|NZ_CP047787.1_877036_877966_-	cd08601, GDPD_SaGlpQ_like, Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins	NA|460aa|down_1|NZ_CP047787.1_878207_879587_-	PRK00855, PRK00855, argininosuccinate lyase; Provisional	NA|402aa|down_2|NZ_CP047787.1_879576_880782_-	PRK00509, PRK00509, argininosuccinate synthase; Provisional	NA|444aa|down_3|NZ_CP047787.1_881132_882464_+	PRK14097, pgi, glucose-6-phosphate isomerase; Provisional	NA|192aa|down_4|NZ_CP047787.1_883389_883965_+	COG0398, COG0398, Uncharacterized conserved protein [Function unknown]	NA|175aa|down_5|NZ_CP047787.1_883969_884494_+	TIGR02227, Inactive_signal_peptidase_IA	NA|192aa|down_6|NZ_CP047787.1_884509_885085_+	TIGR02227, Inactive_signal_peptidase_IA	NA|1159aa|down_7|NZ_CP047787.1_885244_888721_+	TIGR02773, ATP-dependent_helicase/deoxyribonuclease_subunit_B, helicase-exonuclease AddAB, AddB subunit	NA|1218aa|down_8|NZ_CP047787.1_888721_892375_+	TIGR02785, ATP-dependent_helicase/nuclease_subunit_A, helicase-exonuclease AddAB, AddA subunit, Firmicutes type	NA|301aa|down_9|NZ_CP047787.1_892540_893443_+	COG0179, MhpD, 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport, and catabolism]
GCF_009912455.1_ASM991245v1	NZ_CP047787	Staphylococcus aureus strain UP_1108 chromosome, complete genome	4	2161019-2161157	4	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	TTTTTAATATTTTTCTTTTGAGTTACTCGAAAATTTTTCTCTTTACTCGAA	51	1	1	2161070-2161106	NZ_CP047787.1_2160981-2161017	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|93aa|up_7|NZ_CP047787.1_2153068_2153347_+,NA|67aa|up_1|NZ_CP047787.1_2159703_2159904_+,NA|61aa|up_0|NZ_CP047787.1_2159885_2160068_-,NA	NA|807aa|up_9|NZ_CP047787.1_2148720_2151141_+	cd01083, GAG_Lyase, Glycosaminoglycan (GAG) polysaccharide lyase family	NA|285aa|up_8|NZ_CP047787.1_2151339_2152194_-	COG0739, NlpD, Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]	NA|93aa|up_7|NZ_CP047787.1_2153068_2153347_+	NA	NA|506aa|up_6|NZ_CP047787.1_2153356_2154874_+	cd04949, GT4_GtfA-like, accessory Sec system glycosyltransferase GtfA and similar proteins	NA|272aa|up_5|NZ_CP047787.1_2155098_2155914_-	cd02605, HAD_SPP, sucrose-phosphatase, similar to Synechocystis sp PCC 6803 SPP	NA|142aa|up_4|NZ_CP047787.1_2156208_2156634_+	pfam03642, MAP, MAP domain	NA|235aa|up_3|NZ_CP047787.1_2157009_2157714_-	COG3527, AlsD, Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport, and catabolism]	NA|555aa|up_2|NZ_CP047787.1_2157750_2159415_-	PRK08617, PRK08617, acetolactate synthase AlsS	NA|67aa|up_1|NZ_CP047787.1_2159703_2159904_+	NA	NA|61aa|up_0|NZ_CP047787.1_2159885_2160068_-	NA	NA|133aa|down_0|NZ_CP047787.1_2162930_2163329_-	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|146aa|down_1|NZ_CP047787.1_2163342_2163780_-	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|268aa|down_2|NZ_CP047787.1_2164019_2164823_-	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|269aa|down_3|NZ_CP047787.1_2164827_2165634_-	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|287aa|down_4|NZ_CP047787.1_2165623_2166484_-	PRK13646, cbiO, energy-coupling factor transporter ATPase	NA|270aa|down_5|NZ_CP047787.1_2166480_2167290_-	PRK13648, cbiO, cobalt transporter ATP-binding subunit; Provisional	NA|123aa|down_6|NZ_CP047787.1_2167827_2168196_-	PRK05591, rplQ, 50S ribosomal protein L17; Validated	NA|315aa|down_7|NZ_CP047787.1_2168212_2169157_-	PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional	NA|130aa|down_8|NZ_CP047787.1_2169231_2169621_-	PRK05309, PRK05309, 30S ribosomal protein S11; Validated	NA|122aa|down_9|NZ_CP047787.1_2169644_2170010_-	PRK05179, rpsM, 30S ribosomal protein S13; Validated
GCF_009912455.1_ASM991245v1	NZ_CP047787	Staphylococcus aureus strain UP_1108 chromosome, complete genome	5	2352162-2352255	5	CRISPRCasFinder	no		cas3,DEDDh,DinG,csa3,WYL	Orphan	TTCTTCAAATTTATTTGTTAGAAAGG	26	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,DinG,csa3,WYL	NA|35aa|up_2|NZ_CP047787.1_2349883_2349988_+,NA|35aa|down_0|NZ_CP047787.1_2352449_2352554_-	NA|200aa|up_9|NZ_CP047787.1_2343360_2343960_-	COG1651, DsbG, Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]	NA|121aa|up_8|NZ_CP047787.1_2343978_2344341_-	pfam14729, DUF4467, Domain of unknown function with cystatin-like fold (DUF4467)	NA|417aa|up_7|NZ_CP047787.1_2344595_2345846_+	pfam02388, FemAB, FemAB family	NA|244aa|up_6|NZ_CP047787.1_2345942_2346674_-	COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]	NA|240aa|up_5|NZ_CP047787.1_2346670_2347390_-	COG0765, HisM, ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]	NA|260aa|up_4|NZ_CP047787.1_2347370_2348150_-	cd13711, PBP2_Ngo0372_TcyA, Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold	NA|480aa|up_3|NZ_CP047787.1_2348270_2349710_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|35aa|up_2|NZ_CP047787.1_2349883_2349988_+	NA	NA|229aa|up_1|NZ_CP047787.1_2350141_2350828_-	PRK14119, gpmA, phosphoglyceromutase; Provisional	NA|289aa|up_0|NZ_CP047787.1_2351154_2352021_-	COG0053, MMT1, Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]	NA|35aa|down_0|NZ_CP047787.1_2352449_2352554_-	NA	NA|438aa|down_1|NZ_CP047787.1_2352648_2353962_+	pfam11621, Sbi-IV, C3 binding domain 4 of IgG-bind protein SBI	NA|310aa|down_2|NZ_CP047787.1_2354497_2355427_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|316aa|down_3|NZ_CP047787.1_2355994_2356942_+	pfam07968, Leukocidin, Leukocidin/Hemolysin toxin family	NA|326aa|down_4|NZ_CP047787.1_2356943_2357921_+	TIGR01002, synergohymenotropic_toxin, beta-channel forming cytolysin	NA|156aa|down_5|NZ_CP047787.1_2357979_2358447_-	pfam06177, QueT, QueT transporter	NA|231aa|down_6|NZ_CP047787.1_2358457_2359150_-	COG1424, BioW, Pimeloyl-CoA synthetase [Coenzyme metabolism]	NA|372aa|down_7|NZ_CP047787.1_2359160_2360276_-	COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]	NA|336aa|down_8|NZ_CP047787.1_2360253_2361261_-	PRK06256, PRK06256, biotin synthase; Validated	NA|453aa|down_9|NZ_CP047787.1_2361262_2362621_-	TIGR00508, hypothetical_protein_DESPIG_00326, adenosylmethionine-8-amino-7-oxononanoate transaminase
