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
GCA_002863905.1_ASM286390v1	CP024892	Rhodococcus ruber strain YYL plasmid pYYL1.1, complete sequence	1	198090-198405	1,1	CRT,PILER-CR	no	cas10,csm3gr7,cas1,cas2	csa3,cas10,csm3gr7,cas1,cas2	Type III-D,Type III-C,Type III-B,Type III-A	GTTTCTGTGCCCGTAGGCGAATGGAGCACTGTCGAC,GTTTCTGTGCCCGTAGGCGAATGGAGCACTGTCGACC	36,37	0	0	NA	NA	NA:NA	4,3	4	TypeIII-D,TypeIII-C,TypeIII-B,TypeIII-A	WYL,cas4,DEDDh,c2c9_V-U4,DinG,csa3,cas3,Cas9_archaeal,cas10,csm3gr7,cas1,cas2	NA|578aa|up_8|CP024892.1_184801_186535_+,NA|243aa|up_6|CP024892.1_188069_188798_+,NA|151aa|up_4|CP024892.1_190972_191425_-,NA|379aa|up_1|CP024892.1_194396_195533_-,NA|89aa|down_3|CP024892.1_202207_202474_+,NA|99aa|down_4|CP024892.1_202470_202767_+,NA|83aa|down_5|CP024892.1_204819_205068_+,NA|82aa|down_7|CP024892.1_206406_206652_+,NA|82aa|down_8|CP024892.1_206818_207064_-,NA|64aa|down_9|CP024892.1_207208_207400_-	csm3gr7|224aa|up_9|CP024892.1_184126_184798_+	pfam03787, RAMPs, RAMP superfamily	NA|578aa|up_8|CP024892.1_184801_186535_+	NA	NA|514aa|up_7|CP024892.1_186531_188073_+	cd09726, RAMP_I_III, CRISPR/Cas system-associated RAMP superfamily protein	NA|243aa|up_6|CP024892.1_188069_188798_+	NA	csm3gr7|710aa|up_5|CP024892.1_188794_190924_+	TIGR03986, CRISPR-associated_protein, CRISPR-associated protein	NA|151aa|up_4|CP024892.1_190972_191425_-	NA	NA|261aa|up_3|CP024892.1_191450_192233_-	TIGR02169, chromosome_segregation_protein_related_ptotein, chromosome segregation protein SMC, primarily archaeal type	NA|697aa|up_2|CP024892.1_192242_194333_-	TIGR02710, conserved_hypothetical_protein, CRISPR-associated protein, TIGR02710 family	NA|379aa|up_1|CP024892.1_194396_195533_-	NA	NA|685aa|up_0|CP024892.1_195731_197786_-	cd09747, Csx1_III-U, CRISPR/Cas system-associated protein Csx1	cas1|523aa|down_0|CP024892.1_199079_200648_+	cd09634, Cas1_I-II-III, CRISPR/Cas system-associated protein Cas1	cas2|98aa|down_1|CP024892.1_200665_200959_+	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2	NA|266aa|down_2|CP024892.1_201140_201937_-	pfam13340, DUF4096, Putative transposase of IS4/5 family (DUF4096)	NA|89aa|down_3|CP024892.1_202207_202474_+	NA	NA|99aa|down_4|CP024892.1_202470_202767_+	NA	NA|83aa|down_5|CP024892.1_204819_205068_+	NA	NA|243aa|down_6|CP024892.1_205155_205884_-	cd03144, GATase1_ScBLP_like, Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP)	NA|82aa|down_7|CP024892.1_206406_206652_+	NA	NA|82aa|down_8|CP024892.1_206818_207064_-	NA	NA|64aa|down_9|CP024892.1_207208_207400_-	NA
GCA_002863905.1_ASM286390v1	CP024892	Rhodococcus ruber strain YYL plasmid pYYL1.1, complete sequence	2	202838-203216	1,2,2	CRISPRCasFinder,PILER-CR,CRT	no	csm3gr7,cas1,cas2	csa3,cas10,csm3gr7,cas1,cas2	Type III-A	GTTTCTGTGCCCGTAGGCAGGTAGAGCGCTGTCGAC,GTTTCTGTGCCCGTAGGCAGGTAGAGCGCTGTCGAC,GTTTCTGTGCCCGTAGGCAGGTAGAGCGCTGTCGAC	36,36,36	0	0	NA	NA	NA:NA:NA	5,4,4	5	TypeIII-A	WYL,cas4,DEDDh,c2c9_V-U4,DinG,csa3,cas3,Cas9_archaeal,cas10,csm3gr7,cas1,cas2	NA|151aa|up_9|CP024892.1_190972_191425_-,NA|379aa|up_6|CP024892.1_194396_195533_-,NA|89aa|up_1|CP024892.1_202207_202474_+,NA|99aa|up_0|CP024892.1_202470_202767_+,NA|83aa|down_0|CP024892.1_204819_205068_+,NA|82aa|down_2|CP024892.1_206406_206652_+,NA|82aa|down_3|CP024892.1_206818_207064_-,NA|64aa|down_4|CP024892.1_207208_207400_-,NA|62aa|down_6|CP024892.1_209898_210084_-	NA|151aa|up_9|CP024892.1_190972_191425_-	NA	NA|261aa|up_8|CP024892.1_191450_192233_-	TIGR02169, chromosome_segregation_protein_related_ptotein, chromosome segregation protein SMC, primarily archaeal type	NA|697aa|up_7|CP024892.1_192242_194333_-	TIGR02710, conserved_hypothetical_protein, CRISPR-associated protein, TIGR02710 family	NA|379aa|up_6|CP024892.1_194396_195533_-	NA	NA|685aa|up_5|CP024892.1_195731_197786_-	cd09747, Csx1_III-U, CRISPR/Cas system-associated protein Csx1	cas1|523aa|up_4|CP024892.1_199079_200648_+	cd09634, Cas1_I-II-III, CRISPR/Cas system-associated protein Cas1	cas2|98aa|up_3|CP024892.1_200665_200959_+	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2	NA|266aa|up_2|CP024892.1_201140_201937_-	pfam13340, DUF4096, Putative transposase of IS4/5 family (DUF4096)	NA|89aa|up_1|CP024892.1_202207_202474_+	NA	NA|99aa|up_0|CP024892.1_202470_202767_+	NA	NA|83aa|down_0|CP024892.1_204819_205068_+	NA	NA|243aa|down_1|CP024892.1_205155_205884_-	cd03144, GATase1_ScBLP_like, Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP)	NA|82aa|down_2|CP024892.1_206406_206652_+	NA	NA|82aa|down_3|CP024892.1_206818_207064_-	NA	NA|64aa|down_4|CP024892.1_207208_207400_-	NA	NA|287aa|down_5|CP024892.1_207799_208660_-	TIGR02168, Chromosome_partition_protein_Smc, chromosome segregation protein SMC, common bacterial type	NA|62aa|down_6|CP024892.1_209898_210084_-	NA	NA|226aa|down_7|CP024892.1_210103_210781_-	TIGR04211, hypothetical_protein, SH3 domain protein	NA|612aa|down_8|CP024892.1_210777_212613_-	cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-terminal catalytic domain	NA|382aa|down_9|CP024892.1_212609_213755_-	cd01186, INT_tnpA_C_Tn554, Putative Transposase A from transposon Tn554, C-terminal catalytic domain
GCA_002863905.1_ASM286390v1	CP024890	Rhodococcus ruber strain YYL chromosome, complete genome	1	1592772-1592889	1	CRISPRCasFinder	no		WYL,cas4,DEDDh,c2c9_V-U4,DinG,csa3,cas3,Cas9_archaeal	Orphan	ACCACGCGATCCGGCACCGCGAAATCCA	28	1	3	1592800-1592816|1592800-1592816|1592800-1592816	CP024890.1_3280363-3280347|CP024890.1_4747183-4747199|CP024892.1_186031-186047	NA	2	2	Orphan	WYL,cas4,DEDDh,c2c9_V-U4,DinG,csa3,cas3,Cas9_archaeal,cas10,csm3gr7,cas1,cas2	NA|81aa|up_8|CP024890.1_1582631_1582874_+,NA|63aa|up_5|CP024890.1_1584357_1584546_-,NA|143aa|down_0|CP024890.1_1593143_1593572_+	NA|140aa|up_9|CP024890.1_1582053_1582473_-	COG1278, CspC, Cold shock proteins [Transcription]	NA|81aa|up_8|CP024890.1_1582631_1582874_+	NA	NA|131aa|up_7|CP024890.1_1582870_1583263_+	PRK11770, PRK11770, YccF domain-containing protein	NA|195aa|up_6|CP024890.1_1583708_1584293_+	pfam06737, Transglycosylas, Transglycosylase-like domain	NA|63aa|up_5|CP024890.1_1584357_1584546_-	NA	NA|761aa|up_4|CP024890.1_1584606_1586889_+	pfam13625, Helicase_C_3, Helicase conserved C-terminal domain	NA|553aa|up_3|CP024890.1_1586965_1588624_+	COG1061, SSL2, DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]	NA|223aa|up_2|CP024890.1_1588631_1589300_-	COG4565, CitB, Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]	NA|558aa|up_1|CP024890.1_1589281_1590955_-	COG3290, CitA, Signal transduction histidine kinase regulating citrate/malate metabolism [Signal transduction mechanisms]	NA|469aa|up_0|CP024890.1_1591023_1592430_-	COG2851, CitM, H+/citrate symporter [Energy production and conversion]	NA|143aa|down_0|CP024890.1_1593143_1593572_+	NA	NA|216aa|down_1|CP024890.1_1593698_1594346_+	pfam11580, DUF3239, Protein of unknown function (DUF3239)	NA|188aa|down_2|CP024890.1_1594348_1594912_+	pfam13302, Acetyltransf_3, Acetyltransferase (GNAT) domain	NA|329aa|down_3|CP024890.1_1594925_1595912_-	TIGR03560, F420_Rv1855c, probable F420-dependent oxidoreductase, Rv1855c family	NA|450aa|down_4|CP024890.1_1596015_1597365_-	TIGR03860, FMN_nitrolo, FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family	NA|291aa|down_5|CP024890.1_1597398_1598271_-	COG0600, TauC, ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]	NA|273aa|down_6|CP024890.1_1598263_1599082_-	cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of the nitrate and sulfonate transporters	NA|304aa|down_7|CP024890.1_1600517_1601429_+	PRK09636, PRK09636, RNA polymerase sigma factor SigJ; Provisional	NA|138aa|down_8|CP024890.1_1601439_1601853_+	cd07251, VOC_like, uncharacterized subfamily of vicinal oxygen chelate (VOC) family	NA|204aa|down_9|CP024890.1_1601834_1602446_-	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]
GCA_002863905.1_ASM286390v1	CP024890	Rhodococcus ruber strain YYL chromosome, complete genome	6	4652130-4652226	6	CRISPRCasFinder	no		WYL,cas4,DEDDh,c2c9_V-U4,DinG,csa3,cas3,Cas9_archaeal	Orphan	GCGCGGTTCAGCCGGCGCGCACAGCGCGGT	30	0	0	NA	NA	NA	1	1	Orphan	WYL,cas4,DEDDh,c2c9_V-U4,DinG,csa3,cas3,Cas9_archaeal,cas10,csm3gr7,cas1,cas2	NA,NA	NA|247aa|up_9|CP024890.1_4646252_4646993_-	COG1414, IclR, Transcriptional regulator [Transcription]	NA|207aa|up_8|CP024890.1_4647074_4647695_+	pfam01987, AIM24, Mitochondrial biogenesis AIM24	NA|234aa|up_7|CP024890.1_4647703_4648405_+	pfam01987, AIM24, Mitochondrial biogenesis AIM24	NA|252aa|up_6|CP024890.1_4648401_4649157_+	pfam01987, AIM24, Mitochondrial biogenesis AIM24	NA|66aa|up_5|CP024890.1_4649330_4649528_+	pfam04324, Fer2_BFD, BFD-like [2Fe-2S] binding domain	NA|159aa|up_4|CP024890.1_4649573_4650050_+	cd00907, Bacterioferritin, Bacterioferritin, ferritin-like diiron-binding domain	NA|155aa|up_3|CP024890.1_4650046_4650511_+	COG2128, COG2128, Uncharacterized conserved protein [Function unknown]	NA|154aa|up_2|CP024890.1_4650556_4651018_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|97aa|up_1|CP024890.1_4651035_4651326_+	pfam14542, Acetyltransf_CG, GCN5-related N-acetyl-transferase	NA|260aa|up_0|CP024890.1_4651349_4652129_+	TIGR03704, PrmC_rel_meth, putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific	NA|174aa|down_0|CP024890.1_4652976_4653498_+	pfam09350, DUF1992, Domain of unknown function (DUF1992)	NA|303aa|down_1|CP024890.1_4653731_4654640_+	cd07750, PolyPPase_VTC_like, Polyphosphate(polyP) polymerase domain of yeast vacuolar transport chaperone (VTC) proteins VTC-2, -3 and- 4, and similar proteins	NA|226aa|down_2|CP024890.1_4654682_4655360_+	pfam16316, DUF4956, Domain of unknown function (DUF4956)	NA|482aa|down_3|CP024890.1_4655455_4656901_+	COG5337, CotH, Spore coat assembly protein [Cell envelope biogenesis, outer membrane]	NA|194aa|down_4|CP024890.1_4657151_4657733_+	pfam13671, AAA_33, AAA domain	NA|139aa|down_5|CP024890.1_4657960_4658377_+	PRK09648, PRK09648, RNA polymerase sigma factor ShbA	NA|247aa|down_6|CP024890.1_4658584_4659325_+	pfam11139, SfLAP, Sap, sulfolipid-1-addressing protein	NA|394aa|down_7|CP024890.1_4659423_4660605_+	pfam13191, AAA_16, AAA ATPase domain	NA|395aa|down_8|CP024890.1_4660610_4661795_-	COG1940, NagC, Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]	NA|488aa|down_9|CP024890.1_4661963_4663427_+	PRK05722, PRK05722, glucose-6-phosphate 1-dehydrogenase; Validated
