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_010727945.1_ASM1072794v1	NZ_AP022569	Mycobacterium cookii strain JCM 12404	1	581714-581794	1	CRISPRCasFinder	no		WYL,cas4,DEDDh,csa3,DinG,cas3	Orphan	CGGGGCGTTTCCGCCGCCTGCCCC	24	0	0	NA	NA	NA	1	1	Orphan	WYL,cas4,DEDDh,csa3,DinG,cas3	NA|171aa|up_6|NZ_AP022569.1_575873_576386_-,NA|151aa|up_1|NZ_AP022569.1_580408_580861_-,NA	NA|125aa|up_9|NZ_AP022569.1_571201_571576_+	COG4747, COG4747, ACT domain-containing protein [General function prediction only]	NA|269aa|up_8|NZ_AP022569.1_571675_572482_+	pfam13622, 4HBT_3, Thioesterase-like superfamily	NA|1039aa|up_7|NZ_AP022569.1_572744_575861_+	PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed	NA|171aa|up_6|NZ_AP022569.1_575873_576386_-	NA	NA|463aa|up_5|NZ_AP022569.1_576440_577829_+	PRK03348, PRK03348, DNA polymerase IV; Provisional	NA|307aa|up_4|NZ_AP022569.1_577793_578714_-	cd08964, L-asparaginase_II, Type II (periplasmic) bacterial L-asparaginase	NA|234aa|up_3|NZ_AP022569.1_578781_579483_+	PRK14764, PRK14764, lipoprotein signal peptidase; Provisional	NA|309aa|up_2|NZ_AP022569.1_579479_580406_+	TIGR00005, Ribosomal_large_subunit_pseudouridine_synthase_D, pseudouridine synthase, RluA family	NA|151aa|up_1|NZ_AP022569.1_580408_580861_-	NA	NA|252aa|up_0|NZ_AP022569.1_580887_581643_-	pfam08241, Methyltransf_11, Methyltransferase domain	NA|136aa|down_0|NZ_AP022569.1_582643_583051_-	cd00454, TrHb1_N, truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 1 (N)	NA|339aa|down_1|NZ_AP022569.1_583209_584226_+	PRK07201, PRK07201, SDR family oxidoreductase	NA|268aa|down_2|NZ_AP022569.1_584233_585037_+	COG0300, DltE, Short-chain dehydrogenases of various substrate specificities [General function prediction only]	NA|144aa|down_3|NZ_AP022569.1_585036_585468_+	pfam10604, Polyketide_cyc2, Polyketide cyclase / dehydrase and lipid transport	NA|964aa|down_4|NZ_AP022569.1_585524_588416_+	TIGR00833, Putative_membrane_protein_ActII-3, Transport protein	NA|1181aa|down_5|NZ_AP022569.1_588428_591971_+	PRK05673, dnaE, DNA polymerase III subunit alpha; Validated	NA|274aa|down_6|NZ_AP022569.1_591980_592802_-	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|606aa|down_7|NZ_AP022569.1_592852_594670_+	COG1022, FAA1, Long-chain acyl-CoA synthetases (AMP-forming) [Lipid metabolism]	NA|409aa|down_8|NZ_AP022569.1_594672_595899_-	cd03506, Delta6-FADS-like, The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria	NA|146aa|down_9|NZ_AP022569.1_596126_596564_+	pfam04075, F420H2_quin_red, F420H(2)-dependent quinone reductase
GCF_010727945.1_ASM1072794v1	NZ_AP022569	Mycobacterium cookii strain JCM 12404	2	2690717-2690793	2	CRISPRCasFinder	no	csa3	WYL,cas4,DEDDh,csa3,DinG,cas3	Type I-A	TGAGTACCGCCGACGACGATGCAGAG	26	1	3	2690743-2690767|2690743-2690767|2690743-2690767	NZ_AP022569.1_2165543-2165567|NZ_AP022569.1_1455288-1455264|NZ_AP022569.1_3669291-3669267	NA	1	1	Orphan	WYL,cas4,DEDDh,csa3,DinG,cas3	NA,NA	NA|311aa|up_9|NZ_AP022569.1_2682470_2683403_-	TIGR00974, 3a0107s02c, phosphate ABC transporter, permease protein PstA	NA|345aa|up_8|NZ_AP022569.1_2683399_2684434_-	TIGR02138, phosphate_transport_system_permease_protein_PstC, phosphate ABC transporter, permease protein PstC	NA|371aa|up_7|NZ_AP022569.1_2684430_2685543_-	TIGR00975, precursor_PBP-3_PstS-3_Antigen_Ag88	NA|297aa|up_6|NZ_AP022569.1_2685633_2686524_-	TIGR03448, mycothiol_MshD, mycothiol synthase	NA|254aa|up_5|NZ_AP022569.1_2686520_2687282_-	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|269aa|up_4|NZ_AP022569.1_2687415_2688222_+	pfam11209, DUF2993, Protein of unknown function (DUF2993)	NA|139aa|up_3|NZ_AP022569.1_2688330_2688747_+	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|154aa|up_2|NZ_AP022569.1_2688969_2689431_+	pfam14340, DUF4395, Domain of unknown function (DUF4395)	NA|278aa|up_1|NZ_AP022569.1_2689454_2690288_+	COG2897, SseA, Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]	NA|101aa|up_0|NZ_AP022569.1_2690289_2690592_+	pfam07210, DUF1416, Protein of unknown function (DUF1416)	NA|288aa|down_0|NZ_AP022569.1_2691703_2692567_-	PRK07849, PRK07849, aminodeoxychorismate lyase	NA|365aa|down_1|NZ_AP022569.1_2692615_2693710_+	COG0354, COG0354, Predicted aminomethyltransferase related to GcvT [General function prediction only]	NA|56aa|down_2|NZ_AP022569.1_2693844_2694012_+	pfam11273, DUF3073, Protein of unknown function (DUF3073)	NA|360aa|down_3|NZ_AP022569.1_2694048_2695128_-	PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase; Provisional	NA|518aa|down_4|NZ_AP022569.1_2695193_2696747_-	PRK07847, PRK07847, amidophosphoribosyltransferase; Provisional	NA|523aa|down_5|NZ_AP022569.1_2696928_2698497_-	COG1233, COG1233, Phytoene dehydrogenase and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]	NA|200aa|down_6|NZ_AP022569.1_2698580_2699180_+	TIGR03968, transcriptional_regulator_TetR_family, mycofactocin system transcriptional regulator	NA|132aa|down_7|NZ_AP022569.1_2700284_2700680_-	pfam17844, SCP_3, Bacterial SCP ortholog	NA|758aa|down_8|NZ_AP022569.1_2700676_2702950_-	PRK01213, PRK01213, phosphoribosylformylglycinamidine synthase subunit PurL	NA|270aa|down_9|NZ_AP022569.1_2702986_2703796_-	pfam17765, MLTR_LBD, MmyB-like transcription regulator ligand binding domain
GCF_010727945.1_ASM1072794v1	NZ_AP022569	Mycobacterium cookii strain JCM 12404	3	2982522-2982622	3	CRISPRCasFinder	no	cas3	WYL,cas4,DEDDh,csa3,DinG,cas3	Unclear	CTGCATCGTCACCGGCGCAGATCA	24	0	0	NA	NA	NA	1	1	Unclear	WYL,cas4,DEDDh,csa3,DinG,cas3	NA|138aa|up_8|NZ_AP022569.1_2972706_2973120_-,NA|193aa|up_6|NZ_AP022569.1_2976236_2976815_-,NA|251aa|down_3|NZ_AP022569.1_2987336_2988089_-,NA|220aa|down_9|NZ_AP022569.1_2995348_2996008_-	NA|549aa|up_9|NZ_AP022569.1_2971041_2972688_+	cd07302, CHD, cyclase homology domain	NA|138aa|up_8|NZ_AP022569.1_2972706_2973120_-	NA	NA|936aa|up_7|NZ_AP022569.1_2973273_2976081_-	PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated	NA|193aa|up_6|NZ_AP022569.1_2976236_2976815_-	NA	NA|68aa|up_5|NZ_AP022569.1_2977020_2977224_-	COG1278, CspC, Cold shock proteins [Transcription]	cas3|779aa|up_4|NZ_AP022569.1_2977560_2979897_+	TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase	NA|340aa|up_3|NZ_AP022569.1_2980019_2981039_+	pfam18621, DUF5628, Family of unknown function (DUF5628)	NA|178aa|up_2|NZ_AP022569.1_2981035_2981569_-	TIGR03816, tadE_like_DECH, helicase/secretion neighborhood TadE-like protein	NA|69aa|up_1|NZ_AP022569.1_2981686_2981893_-	pfam14029, DUF4244, Protein of unknown function (DUF4244)	NA|178aa|up_0|NZ_AP022569.1_2981905_2982439_-	pfam00482, T2SSF, Type II secretion system (T2SS), protein F	NA|388aa|down_0|NZ_AP022569.1_2983410_2984574_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|363aa|down_1|NZ_AP022569.1_2984570_2985659_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|283aa|down_2|NZ_AP022569.1_2986040_2986889_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|251aa|down_3|NZ_AP022569.1_2987336_2988089_-	NA	NA|551aa|down_4|NZ_AP022569.1_2988085_2989738_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]	NA|285aa|down_5|NZ_AP022569.1_2989734_2990589_-	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|309aa|down_6|NZ_AP022569.1_2990581_2991508_-	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|532aa|down_7|NZ_AP022569.1_2991509_2993105_-	cd00995, PBP2_NikA_DppA_OppA_like, The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold	NA|653aa|down_8|NZ_AP022569.1_2993215_2995174_+	PRK00174, PRK00174, acetyl-CoA synthetase; Provisional	NA|220aa|down_9|NZ_AP022569.1_2995348_2996008_-	NA
GCF_010727945.1_ASM1072794v1	NZ_AP022569	Mycobacterium cookii strain JCM 12404	4	3195594-3195679	4	CRISPRCasFinder	no		WYL,cas4,DEDDh,csa3,DinG,cas3	Orphan	AGCTCCGCCAACATCGGGTTGGGCGC	26	0	0	NA	NA	NA	1	1	Orphan	WYL,cas4,DEDDh,csa3,DinG,cas3	NA,NA|108aa|down_0|NZ_AP022569.1_3196288_3196612_+	NA|729aa|up_9|NZ_AP022569.1_3147535_3149722_-	COG1835, COG1835, Predicted acyltransferases [Lipid metabolism]	NA|429aa|up_8|NZ_AP022569.1_3149929_3151216_+	COG1819, COG1819, Glycosyl transferases, related to UDP-glucuronosyltransferase [Carbohydrate transport and metabolism / Signal transduction mechanisms]	NA|3650aa|up_7|NZ_AP022569.1_3151628_3162578_+	COG3321, COG3321, Polyketide synthase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]	NA|284aa|up_6|NZ_AP022569.1_3162643_3163495_+	pfam13649, Methyltransf_25, Methyltransferase domain	NA|83aa|up_5|NZ_AP022569.1_3163629_3163878_+	pfam03621, MbtH, MbtH-like protein	NA|1517aa|up_4|NZ_AP022569.1_3163867_3168418_+	PRK12467, PRK12467, peptide synthase; Provisional	NA|545aa|up_3|NZ_AP022569.1_3168404_3170039_+	cd19543, DCL_NRPS, DCL-type Condensation domain of nonribosomal peptide synthetases (NRPSs), which catalyzes the condensation between a D-aminoacyl/peptidyl-PCP donor and a L-aminoacyl-PCP acceptor	NA|2297aa|up_2|NZ_AP022569.1_3174011_3180902_+	PRK12467, PRK12467, peptide synthase; Provisional	NA|225aa|up_1|NZ_AP022569.1_3184215_3184890_-	COG2020, STE14, Putative protein-S-isoprenylcysteine methyltransferase [Posttranslational modification, protein turnover, chaperones]	NA|3238aa|up_0|NZ_AP022569.1_3185220_3194934_+	PRK05850, PRK05850, acyl-CoA synthetase; Validated	NA|108aa|down_0|NZ_AP022569.1_3196288_3196612_+	NA	NA|606aa|down_1|NZ_AP022569.1_3196923_3198741_+	pfam13454, NAD_binding_9, FAD-NAD(P)-binding	NA|428aa|down_2|NZ_AP022569.1_3198745_3200029_+	PRK02186, PRK02186, argininosuccinate lyase; Provisional	NA|311aa|down_3|NZ_AP022569.1_3200030_3200963_+	PRK05368, PRK05368, homoserine O-succinyltransferase; Provisional	NA|429aa|down_4|NZ_AP022569.1_3200967_3202254_+	COG2873, MET17, O-acetylhomoserine sulfhydrylase [Amino acid transport and metabolism]	NA|555aa|down_5|NZ_AP022569.1_3202396_3204061_+	TIGR03101, hydr2_PEP, exosortase A system-associated hydrolase 2	NA|158aa|down_6|NZ_AP022569.1_3204070_3204544_-	COG0736, AcpS, Phosphopantetheinyl transferase (holo-ACP synthase) [Lipid metabolism]	NA|82aa|down_7|NZ_AP022569.1_3204543_3204789_-	PRK07081, PRK07081, acyl carrier protein; Provisional	NA|304aa|down_8|NZ_AP022569.1_3204826_3205738_-	pfam05721, PhyH, Phytanoyl-CoA dioxygenase (PhyH)	NA|310aa|down_9|NZ_AP022569.1_3205830_3206760_+	TIGR03621, F420_MSMEG_2516, probable F420-dependent oxidoreductase, MSMEG_2516 family
GCF_010727945.1_ASM1072794v1	NZ_AP022569	Mycobacterium cookii strain JCM 12404	5	5196112-5196257	5	CRISPRCasFinder	no		WYL,cas4,DEDDh,csa3,DinG,cas3	Orphan	TTCGGCAACGGCGGTGACGGGGG	23	0	0	NA	NA	NA	2	2	Orphan	WYL,cas4,DEDDh,csa3,DinG,cas3	NA|182aa|up_8|NZ_AP022569.1_5186838_5187384_+,NA|276aa|up_1|NZ_AP022569.1_5194177_5195005_+,NA|284aa|down_2|NZ_AP022569.1_5200911_5201763_+,NA|129aa|down_4|NZ_AP022569.1_5202645_5203032_-	NA|321aa|up_9|NZ_AP022569.1_5185860_5186823_+	TIGR04171, ribonucleotide-diphosphate_reductase_subunit_beta, ribonucleoside-diphosphate reductase, class 1b, beta subunit	NA|182aa|up_8|NZ_AP022569.1_5186838_5187384_+	NA	NA|106aa|up_7|NZ_AP022569.1_5187562_5187880_+	pfam11829, DUF3349, Protein of unknown function (DUF3349)	NA|347aa|up_6|NZ_AP022569.1_5187868_5188909_-	cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD)	NA|363aa|up_5|NZ_AP022569.1_5189038_5190127_-	cd01146, FhuD, Fe3+-siderophore binding domain FhuD	NA|582aa|up_4|NZ_AP022569.1_5190298_5192044_+	cd01662, Ubiquinol_Oxidase_I, Ubiquinol oxidase subunit I	NA|410aa|up_3|NZ_AP022569.1_5192075_5193305_+	cd07500, HAD_PSP, phosphoserine phosphatase (PSP), similar to Methanococcus Jannaschii PSP and Saccharomyces cerevisiae SER2p	NA|286aa|up_2|NZ_AP022569.1_5193320_5194178_+	COG1119, ModF, ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]	NA|276aa|up_1|NZ_AP022569.1_5194177_5195005_+	NA	NA|230aa|up_0|NZ_AP022569.1_5194992_5195682_+	PRK05869, PRK05869, enoyl-CoA hydratase; Validated	NA|323aa|down_0|NZ_AP022569.1_5197828_5198797_+	pfam08241, Methyltransf_11, Methyltransferase domain	NA|411aa|down_1|NZ_AP022569.1_5198730_5199963_+	pfam18096, Thump_like, THUMP domain-like	NA|284aa|down_2|NZ_AP022569.1_5200911_5201763_+	NA	NA|237aa|down_3|NZ_AP022569.1_5201938_5202649_+	pfam11738, DUF3298, Protein of unknown function (DUF3298)	NA|129aa|down_4|NZ_AP022569.1_5202645_5203032_-	NA	NA|461aa|down_5|NZ_AP022569.1_5203069_5204452_-	COG1520, COG1520, FOG: WD40-like repeat [Function unknown]	NA|246aa|down_6|NZ_AP022569.1_5204450_5205188_+	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|447aa|down_7|NZ_AP022569.1_5205184_5206525_-	COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]	NA|161aa|down_8|NZ_AP022569.1_5206541_5207024_-	cd15904, TSPO_MBR, Translocator protein (TSPO)/peripheral-type benzodiazepine receptor (MBR) family	NA|171aa|down_9|NZ_AP022569.1_5207117_5207630_+	COG1846, MarR, Transcriptional regulators [Transcription]
