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_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	1	333915-334713	1	CRT	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	CCGCCGGNGCCGCCGGNN	18	0	0	NA	NA	NA	15	15	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|61aa|up_0|NZ_AP018033.1_333430_333613_-,NA	NA|398aa|up_9|NZ_AP018033.1_323608_324802_-	COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]	NA|561aa|up_8|NZ_AP018033.1_324837_326520_+	PRK07788, PRK07788, acyl-CoA synthetase; Validated	NA|732aa|up_7|NZ_AP018033.1_326536_328732_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|378aa|up_6|NZ_AP018033.1_328845_329979_-	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|207aa|up_5|NZ_AP018033.1_329975_330596_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|194aa|up_4|NZ_AP018033.1_330692_331274_+	pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily	NA|242aa|up_3|NZ_AP018033.1_331203_331929_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|307aa|up_2|NZ_AP018033.1_332018_332939_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	NA|143aa|up_1|NZ_AP018033.1_332978_333407_-	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|61aa|up_0|NZ_AP018033.1_333430_333613_-	NA	NA|849aa|down_0|NZ_AP018033.1_336760_339307_-	pfam00934, PE, PE family	NA|537aa|down_1|NZ_AP018033.1_341487_343098_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|303aa|down_2|NZ_AP018033.1_343121_344030_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|632aa|down_3|NZ_AP018033.1_344253_346149_+	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA	NA|539aa|down_4|NZ_AP018033.1_346145_347762_+	pfam05108, T7SS_ESX1_EccB, Type VII secretion system ESX-1, transport TM domain B	NA|1331aa|down_5|NZ_AP018033.1_347758_351751_+	TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa	NA|103aa|down_6|NZ_AP018033.1_351747_352056_+	pfam00934, PE, PE family	NA|514aa|down_7|NZ_AP018033.1_352058_353600_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|98aa|down_8|NZ_AP018033.1_353648_353942_+	TIGR03930, WXG100_ESAT6, WXG100 family type VII secretion target	NA|97aa|down_9|NZ_AP018033.1_353971_354262_+	COG4842, COG4842, Uncharacterized protein conserved in bacteria [Function unknown]
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	2	335098-335208	1	PILER-CR	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	CCGCCGTTGCCGCCGTTGCCGATC	24	0	0	NA	NA	NA	2	2	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|61aa|up_0|NZ_AP018033.1_333430_333613_-,NA	NA|398aa|up_9|NZ_AP018033.1_323608_324802_-	COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]	NA|561aa|up_8|NZ_AP018033.1_324837_326520_+	PRK07788, PRK07788, acyl-CoA synthetase; Validated	NA|732aa|up_7|NZ_AP018033.1_326536_328732_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|378aa|up_6|NZ_AP018033.1_328845_329979_-	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|207aa|up_5|NZ_AP018033.1_329975_330596_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|194aa|up_4|NZ_AP018033.1_330692_331274_+	pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily	NA|242aa|up_3|NZ_AP018033.1_331203_331929_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|307aa|up_2|NZ_AP018033.1_332018_332939_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	NA|143aa|up_1|NZ_AP018033.1_332978_333407_-	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|61aa|up_0|NZ_AP018033.1_333430_333613_-	NA	NA|849aa|down_0|NZ_AP018033.1_336760_339307_-	pfam00934, PE, PE family	NA|537aa|down_1|NZ_AP018033.1_341487_343098_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|303aa|down_2|NZ_AP018033.1_343121_344030_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|632aa|down_3|NZ_AP018033.1_344253_346149_+	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA	NA|539aa|down_4|NZ_AP018033.1_346145_347762_+	pfam05108, T7SS_ESX1_EccB, Type VII secretion system ESX-1, transport TM domain B	NA|1331aa|down_5|NZ_AP018033.1_347758_351751_+	TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa	NA|103aa|down_6|NZ_AP018033.1_351747_352056_+	pfam00934, PE, PE family	NA|514aa|down_7|NZ_AP018033.1_352058_353600_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|98aa|down_8|NZ_AP018033.1_353648_353942_+	TIGR03930, WXG100_ESAT6, WXG100 family type VII secretion target	NA|97aa|down_9|NZ_AP018033.1_353971_354262_+	COG4842, COG4842, Uncharacterized protein conserved in bacteria [Function unknown]
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	3	368629-369327	1	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	TTCGCGAAGCCGATGTTGTAGCTGCCGGTGTTG	33	2	2	368917-368958|368992-369024	NZ_AP018033.1_376903-376944|NZ_AP018033.1_375718-375750	NA	10	10	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|101aa|up_4|NZ_AP018033.1_365641_365944_+,NA|161aa|down_1|NZ_AP018033.1_378692_379175_-,NA|410aa|down_5|NZ_AP018033.1_381291_382521_+	NA|262aa|up_9|NZ_AP018033.1_360294_361080_+	PRK14103, PRK14103, trans-aconitate 2-methyltransferase; Provisional	NA|268aa|up_8|NZ_AP018033.1_361068_361872_-	COG4424, COG4424, Uncharacterized protein conserved in bacteria [Function unknown]	NA|466aa|up_7|NZ_AP018033.1_361881_363279_-	cd16027, SGSH, N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase)	NA|606aa|up_6|NZ_AP018033.1_363457_365275_+	pfam00934, PE, PE family	NA|76aa|up_5|NZ_AP018033.1_365417_365645_+	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|101aa|up_4|NZ_AP018033.1_365641_365944_+	NA	NA|74aa|up_3|NZ_AP018033.1_365991_366213_+	PHA01748, PHA01748, hypothetical protein	NA|142aa|up_2|NZ_AP018033.1_366209_366635_+	cd18755, PIN_MtVapC3_VapC21-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC3, VapC21 and related proteins	NA|211aa|up_1|NZ_AP018033.1_366770_367403_+	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|303aa|up_0|NZ_AP018033.1_367399_368308_+	cd09810, LPOR_like_SDR_c_like, light-dependent protochlorophyllide reductase (LPOR)-like, classical (c)-like SDRs	NA|224aa|down_0|NZ_AP018033.1_378033_378705_+	TIGR02476, BluB, 5,6-dimethylbenzimidazole synthase	NA|161aa|down_1|NZ_AP018033.1_378692_379175_-	NA	NA|239aa|down_2|NZ_AP018033.1_379232_379949_+	cd03392, PAP2_like_2, PAP2_like_2 proteins	NA|219aa|down_3|NZ_AP018033.1_380050_380707_+	COG3786, COG3786, Uncharacterized protein conserved in bacteria [Function unknown]	NA|164aa|down_4|NZ_AP018033.1_380776_381268_-	pfam13577, SnoaL_4, SnoaL-like domain	NA|410aa|down_5|NZ_AP018033.1_381291_382521_+	NA	NA|621aa|down_6|NZ_AP018033.1_382675_384538_+	COG0443, DnaK, Molecular chaperone [Posttranslational modification, protein turnover, chaperones]	NA|129aa|down_7|NZ_AP018033.1_384609_384996_+	COG0326, HtpG, Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]	NA|212aa|down_8|NZ_AP018033.1_384998_385634_-	pfam11259, DUF3060, Protein of unknown function (DUF3060)	NA|295aa|down_9|NZ_AP018033.1_385721_386606_+	COG2273, SKN1, Beta-glucanase/Beta-glucan synthetase [Carbohydrate transport and metabolism]
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	4	634276-634413	2	CRT	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	CCGCCGACCACGCCGGTG	18	2	3	634294-634311|634294-634311|634378-634395	NZ_AP018033.1_22466-22483|NZ_AP018033.1_1412890-1412907|NZ_AP018033.1_975949-975966	NA	3	3	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|54aa|up_7|NZ_AP018033.1_625020_625182_-,NA|478aa|up_0|NZ_AP018033.1_631291_632725_-,NA|450aa|down_2|NZ_AP018033.1_636048_637398_-,NA|93aa|down_5|NZ_AP018033.1_638928_639207_-	NA|325aa|up_9|NZ_AP018033.1_622790_623765_+	TIGR03144, cytochrome_c_biogenesis_protein_chloroplast, cytochrome c-type biogenesis protein CcsB	NA|406aa|up_8|NZ_AP018033.1_623806_625024_+	COG0455, flhG, Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]	NA|54aa|up_7|NZ_AP018033.1_625020_625182_-	NA	NA|106aa|up_6|NZ_AP018033.1_625228_625546_+	pfam14012, DUF4229, Protein of unknown function (DUF4229)	NA|582aa|up_5|NZ_AP018033.1_625692_627438_+	pfam00934, PE, PE family	NA|336aa|up_4|NZ_AP018033.1_627466_628474_-	TIGR00747, 3-oxoacyl-_synthase_3, 3-oxoacyl-(acyl-carrier-protein) synthase III	NA|293aa|up_3|NZ_AP018033.1_628555_629434_-	TIGR00751, 14-dihydroxy-2-naphthoate_octaprenyltransferase, 1,4-dihydroxy-2-naphthoate octaprenyltransferase	NA|265aa|up_2|NZ_AP018033.1_629450_630245_+	PRK07823, PRK07823, S-methyl-5'-thioadenosine phosphorylase	NA|347aa|up_1|NZ_AP018033.1_630241_631282_+	cd05256, UDP_AE_SDR_e, UDP-N-acetylglucosamine 4-epimerase, extended (e) SDRs	NA|478aa|up_0|NZ_AP018033.1_631291_632725_-	NA	NA|211aa|down_0|NZ_AP018033.1_634736_635369_+	cd04179, DPM_DPG-synthase_like, DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily	NA|221aa|down_1|NZ_AP018033.1_635365_636028_+	COG3222, COG3222, Uncharacterized protein conserved in bacteria [Function unknown]	NA|450aa|down_2|NZ_AP018033.1_636048_637398_-	NA	NA|381aa|down_3|NZ_AP018033.1_637409_638552_-	PRK07824, PRK07824, o-succinylbenzoate--CoA ligase	NA|101aa|down_4|NZ_AP018033.1_638566_638869_-	pfam11829, DUF3349, Protein of unknown function (DUF3349)	NA|93aa|down_5|NZ_AP018033.1_638928_639207_-	NA	NA|418aa|down_6|NZ_AP018033.1_639203_640457_-	COG0306, PitA, Phosphate/sulphate permeases [Inorganic ion transport and metabolism]	NA|129aa|down_7|NZ_AP018033.1_640576_640963_-	cd07264, VOC_like, uncharacterized subfamily of vicinal oxygen chelate (VOC) family	NA|295aa|down_8|NZ_AP018033.1_641025_641910_-	PRK05866, PRK05866, SDR family oxidoreductase	NA|301aa|down_9|NZ_AP018033.1_642005_642908_-	PRK08321, PRK08321, 1,4-dihydroxy-2-naphthoyl-CoA synthase
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	5	695046-695122	2	CRISPRCasFinder	no	c2c9_V-U4	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type V-U4	TGAGGTGCGGCGTGAGCGCGGGT	23	0	0	NA	NA	NA	1	1	TypeV-U4	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA	NA|136aa|up_9|NZ_AP018033.1_680942_681350_+	cd18696, PIN_MtVapC26-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins	NA|229aa|up_8|NZ_AP018033.1_681409_682096_-	pfam10738, Lpp-LpqN, Probable lipoprotein LpqN	NA|878aa|up_7|NZ_AP018033.1_682249_684883_+	COG3537, COG3537, Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]	NA|796aa|up_6|NZ_AP018033.1_684905_687293_-	pfam03706, LPG_synthase_TM, Lysylphosphatidylglycerol synthase TM region	NA|241aa|up_5|NZ_AP018033.1_687429_688152_+	COG2186, FadR, Transcriptional regulators [Transcription]	NA|266aa|up_4|NZ_AP018033.1_688148_688946_+	COG0767, Ttg2B, ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|296aa|up_3|NZ_AP018033.1_688947_689835_+	COG0767, Ttg2B, ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|405aa|up_2|NZ_AP018033.1_689840_691055_+	pfam11887, Mce4_CUP1, Cholesterol uptake porter CUP1 of Mce4, putative	NA|344aa|up_1|NZ_AP018033.1_691051_692083_+	COG1463, Ttg2C, ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|482aa|up_0|NZ_AP018033.1_692079_693525_+	TIGR00996, Mtu_fam_mce, virulence factor Mce family protein	NA|517aa|down_0|NZ_AP018033.1_696257_697808_+	COG1463, Ttg2C, ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|131aa|down_1|NZ_AP018033.1_697859_698252_-	cd18768, PIN_MtVapC4-C5-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins	NA|86aa|down_2|NZ_AP018033.1_698248_698506_-	COG4118, Phd, Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]	NA|412aa|down_3|NZ_AP018033.1_698688_699924_-	COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General function prediction only]	NA|138aa|down_4|NZ_AP018033.1_700174_700588_-	cd18681, PIN_MtVapC27-VapC40_like, VapC-like PIN domain of Mycobacterium tuberculosis VapC27, and VapC40, and related proteins	NA|79aa|down_5|NZ_AP018033.1_700584_700821_-	COG2002, AbrB, Regulators of stationary/sporulation gene expression [Transcription]	NA|169aa|down_6|NZ_AP018033.1_700924_701431_-	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|157aa|down_7|NZ_AP018033.1_701544_702015_-	PRK10755, PRK10755, two-component system sensor histidine kinase PmrB	NA|254aa|down_8|NZ_AP018033.1_702058_702820_-	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|104aa|down_9|NZ_AP018033.1_702876_703188_+	pfam03413, PepSY, Peptidase propeptide and YPEB domain
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	6	842418-843546	3,3	CRT,CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	NACGGCGGNGCCGGCGGGGCCGGCGG,GGCGGGGCCGGCGGGGCCGGCGGG	26,24	14	52	842621-842642|842666-842684|842666-842684|842666-842684|842666-842684|842819-842840|842819-842840|842460-842474|842460-842474|842460-842474|842460-842474|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842538-842558|842583-842597|842622-842642|842622-842642|842667-842684|842709-842732|842802-842831|842802-842831|842856-842876|842856-842876|842856-842876|842856-842876|842856-842876|842988-843008|843273-843287|843273-843287|843273-843287|843357-843386	NZ_AP018033.1_335919-335898|NZ_AP018033.1_2860852-2860834|NZ_AP018033.1_890039-890021|NZ_AP018033.1_987337-987355|NZ_AP018033.1_1568083-1568065|NZ_AP018033.1_1988580-1988559|NZ_AP018033.1_338702-338681|NZ_AP018033.1_256833-256819|NZ_AP018033.1_336098-336084|NZ_AP018033.1_927995-928009|NZ_AP018033.1_1988942-1988928|NZ_AP018033.1_626245-626265|NZ_AP018033.1_841195-841215|NZ_AP018033.1_1098590-1098570|NZ_AP018033.1_1656049-1656029|NZ_AP018033.1_1988858-1988838|NZ_AP018033.1_2041632-2041612|NZ_AP018033.1_2058575-2058555|NZ_AP018033.1_2943576-2943556|NZ_AP018033.1_3920590-3920610|NZ_AP018033.1_3936437-3936457|NZ_AP018033.1_132026-132046|NZ_AP018033.1_150550-150570|NZ_AP018033.1_1218079-1218099|NZ_AP018033.1_1218964-1218984|NZ_AP018033.1_1490370-1490350|NZ_AP018033.1_1572445-1572425|NZ_AP018033.1_2041752-2041732|NZ_AP018033.1_2058386-2058366|NZ_AP018033.1_2423905-2423885|NZ_AP018033.1_2804102-2804082|NZ_AP018033.1_3152424-3152444|NZ_AP018033.1_3789882-3789902|NZ_AP018033.1_3790461-3790481|NZ_AP018033.1_4080690-4080710|NZ_AP018033.1_1324370-1324356|NZ_AP018033.1_338746-338726|NZ_AP018033.1_335918-335898|NZ_AP018033.1_2860851-2860834|NZ_AP018033.1_1854976-1854953|NZ_AP018033.1_1988597-1988568|NZ_AP018033.1_338719-338690|NZ_AP018033.1_3728522-3728502|NZ_AP018033.1_337606-337586|NZ_AP018033.1_1218673-1218693|NZ_AP018033.1_1636935-1636915|NZ_AP018033.1_1637112-1637092|NZ_AP018033.1_338629-338609|NZ_AP018033.1_168737-168751|NZ_AP018033.1_340009-339995|NZ_AP018033.1_340282-340268|NZ_AP018033.1_2423563-2423534	NA:NA	18,24	24	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|71aa|up_8|NZ_AP018033.1_833362_833575_+,NA|176aa|up_5|NZ_AP018033.1_835439_835967_+,NA|186aa|up_4|NZ_AP018033.1_837492_838050_-,NA|46aa|down_2|NZ_AP018033.1_845730_845868_-,NA|82aa|down_3|NZ_AP018033.1_846026_846272_+,NA|242aa|down_9|NZ_AP018033.1_854734_855460_-	NA|166aa|up_9|NZ_AP018033.1_832868_833366_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|71aa|up_8|NZ_AP018033.1_833362_833575_+	NA	NA|183aa|up_7|NZ_AP018033.1_833723_834272_+	TIGR03086, TIGR03086, TIGR03086 family protein	NA|283aa|up_6|NZ_AP018033.1_834476_835325_+	pfam10774, DUF4226, Domain of unknown function (DUF4226)	NA|176aa|up_5|NZ_AP018033.1_835439_835967_+	NA	NA|186aa|up_4|NZ_AP018033.1_837492_838050_-	NA	NA|169aa|up_3|NZ_AP018033.1_838046_838553_-	pfam12728, HTH_17, Helix-turn-helix domain	NA|49aa|up_2|NZ_AP018033.1_838665_838812_-	TIGR01692, 3-hydroxyisobutyrate_dehydrogenase_mitochondrial, 3-hydroxyisobutyrate dehydrogenase	NA|176aa|up_1|NZ_AP018033.1_838760_839288_+	TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase	NA|785aa|up_0|NZ_AP018033.1_839307_841662_+	pfam00934, PE, PE family	NA|86aa|down_0|NZ_AP018033.1_844940_845198_+	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|143aa|down_1|NZ_AP018033.1_845221_845650_+	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|46aa|down_2|NZ_AP018033.1_845730_845868_-	NA	NA|82aa|down_3|NZ_AP018033.1_846026_846272_+	NA	NA|295aa|down_4|NZ_AP018033.1_846340_847225_-	TIGR01692, 3-hydroxyisobutyrate_dehydrogenase_mitochondrial, 3-hydroxyisobutyrate dehydrogenase	NA|391aa|down_5|NZ_AP018033.1_847235_848408_-	cd01162, IBD, Isobutyryl-CoA dehydrogenase	NA|511aa|down_6|NZ_AP018033.1_848414_849947_-	cd07085, ALDH_F6_MMSDH, Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2	NA|585aa|down_7|NZ_AP018033.1_850152_851907_+	pfam00934, PE, PE family	NA|646aa|down_8|NZ_AP018033.1_852096_854034_-	pfam00823, PPE, PPE family	NA|242aa|down_9|NZ_AP018033.1_854734_855460_-	NA
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	7	843699-844802	4	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	GGCGGGGCCGGCGGGGCCGGCGGG	24	9	25	843792-843824|843849-843866|843891-843911|843936-843956|843936-843956|844020-844040|844020-844040|844065-844085|844065-844085|844155-844175|844155-844175|844155-844175|844155-844175|844155-844175|844155-844175|844155-844175|844155-844175|844155-844175|844155-844175|844155-844175|844155-844175|844155-844175|844368-844385|844548-844568|844548-844568	NZ_AP018033.1_334799-334767|NZ_AP018033.1_481082-481065|NZ_AP018033.1_1988216-1988196|NZ_AP018033.1_1218115-1218135|NZ_AP018033.1_1572283-1572263|NZ_AP018033.1_1218115-1218135|NZ_AP018033.1_1572283-1572263|NZ_AP018033.1_3767994-3768014|NZ_AP018033.1_4080690-4080710|NZ_AP018033.1_3790131-3790151|NZ_AP018033.1_335567-335547|NZ_AP018033.1_335654-335634|NZ_AP018033.1_337327-337307|NZ_AP018033.1_337405-337385|NZ_AP018033.1_338620-338600|NZ_AP018033.1_340360-340340|NZ_AP018033.1_340444-340424|NZ_AP018033.1_2058386-2058366|NZ_AP018033.1_2943477-2943457|NZ_AP018033.1_3916142-3916162|NZ_AP018033.1_840172-840192|NZ_AP018033.1_3042795-3042815|NZ_AP018033.1_1987040-1987023|NZ_AP018033.1_2423039-2423059|NZ_AP018033.1_2921707-2921687	NA	22	22	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|71aa|up_8|NZ_AP018033.1_833362_833575_+,NA|176aa|up_5|NZ_AP018033.1_835439_835967_+,NA|186aa|up_4|NZ_AP018033.1_837492_838050_-,NA|46aa|down_2|NZ_AP018033.1_845730_845868_-,NA|82aa|down_3|NZ_AP018033.1_846026_846272_+,NA|242aa|down_9|NZ_AP018033.1_854734_855460_-	NA|166aa|up_9|NZ_AP018033.1_832868_833366_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|71aa|up_8|NZ_AP018033.1_833362_833575_+	NA	NA|183aa|up_7|NZ_AP018033.1_833723_834272_+	TIGR03086, TIGR03086, TIGR03086 family protein	NA|283aa|up_6|NZ_AP018033.1_834476_835325_+	pfam10774, DUF4226, Domain of unknown function (DUF4226)	NA|176aa|up_5|NZ_AP018033.1_835439_835967_+	NA	NA|186aa|up_4|NZ_AP018033.1_837492_838050_-	NA	NA|169aa|up_3|NZ_AP018033.1_838046_838553_-	pfam12728, HTH_17, Helix-turn-helix domain	NA|49aa|up_2|NZ_AP018033.1_838665_838812_-	TIGR01692, 3-hydroxyisobutyrate_dehydrogenase_mitochondrial, 3-hydroxyisobutyrate dehydrogenase	NA|176aa|up_1|NZ_AP018033.1_838760_839288_+	TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase	NA|785aa|up_0|NZ_AP018033.1_839307_841662_+	pfam00934, PE, PE family	NA|86aa|down_0|NZ_AP018033.1_844940_845198_+	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|143aa|down_1|NZ_AP018033.1_845221_845650_+	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|46aa|down_2|NZ_AP018033.1_845730_845868_-	NA	NA|82aa|down_3|NZ_AP018033.1_846026_846272_+	NA	NA|295aa|down_4|NZ_AP018033.1_846340_847225_-	TIGR01692, 3-hydroxyisobutyrate_dehydrogenase_mitochondrial, 3-hydroxyisobutyrate dehydrogenase	NA|391aa|down_5|NZ_AP018033.1_847235_848408_-	cd01162, IBD, Isobutyryl-CoA dehydrogenase	NA|511aa|down_6|NZ_AP018033.1_848414_849947_-	cd07085, ALDH_F6_MMSDH, Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2	NA|585aa|down_7|NZ_AP018033.1_850152_851907_+	pfam00934, PE, PE family	NA|646aa|down_8|NZ_AP018033.1_852096_854034_-	pfam00823, PPE, PPE family	NA|242aa|down_9|NZ_AP018033.1_854734_855460_-	NA
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	8	929257-930270	4	CRT	no	csa3	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type I-A	CGGGGCCGGCGGNNCCGGCGG	21	1	2	930106-930141|930106-930141	NZ_AP018033.1_678149-678114|NZ_AP018033.1_1214867-1214902	NA	20	20	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA|184aa|down_2|NZ_AP018033.1_934280_934832_-,NA|81aa|down_8|NZ_AP018033.1_940295_940538_+	NA|685aa|up_9|NZ_AP018033.1_916892_918947_-	TIGR00350, Transcriptional_regulator_LytR, cell envelope-related function transcriptional attenuator common domain	NA|390aa|up_8|NZ_AP018033.1_919112_920282_-	TIGR00737, Probable_tRNA-dihydrouridine_synthase, putative TIM-barrel protein, nifR3 family	NA|339aa|up_7|NZ_AP018033.1_920369_921386_-	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|214aa|up_6|NZ_AP018033.1_921547_922189_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|352aa|up_5|NZ_AP018033.1_922269_923325_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|131aa|up_4|NZ_AP018033.1_923376_923769_-	smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon Repressor	NA|141aa|up_3|NZ_AP018033.1_923826_924249_-	COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]	NA|97aa|up_2|NZ_AP018033.1_924210_924501_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|302aa|up_1|NZ_AP018033.1_924605_925511_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|272aa|up_0|NZ_AP018033.1_925529_926345_-	TIGR04255, hypothetical_protein, TIGR04255 family protein	NA|883aa|down_0|NZ_AP018033.1_930539_933188_-	pfam00934, PE, PE family	NA|215aa|down_1|NZ_AP018033.1_933655_934300_+	pfam14032, PknH_C, PknH-like extracellular domain	NA|184aa|down_2|NZ_AP018033.1_934280_934832_-	NA	NA|241aa|down_3|NZ_AP018033.1_934912_935635_-	COG4849, COG4849, Predicted nucleotidyltransferase [General function prediction    only]	NA|343aa|down_4|NZ_AP018033.1_935705_936734_-	COG4861, COG4861, Uncharacterized protein conserved in bacteria [Function unknown]	NA|257aa|down_5|NZ_AP018033.1_937422_938193_+	pfam01427, Peptidase_M15, D-ala-D-ala dipeptidase	NA|271aa|down_6|NZ_AP018033.1_938279_939092_+	pfam13847, Methyltransf_31, Methyltransferase domain	NA|287aa|down_7|NZ_AP018033.1_939159_940020_-	TIGR01250, Proline_iminopeptidase, proline-specific peptidase, Bacillus coagulans-type subfamily	NA|81aa|down_8|NZ_AP018033.1_940295_940538_+	NA	NA|431aa|down_9|NZ_AP018033.1_940814_942107_+	cd17329, MFS_MdtH_MDR_like, Multidrug resistance protein MdtH and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	9	2084617-2084871	5	CRT	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	GCCNCCGTCGCCGCCNNTGCC	21	2	3	2084698-2084715|2084698-2084715|2084788-2084805	NZ_AP018033.1_403198-403181|NZ_AP018033.1_610338-610321|NZ_AP018033.1_3437763-3437746	NA	5	5	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|88aa|up_0|NZ_AP018033.1_2083976_2084240_-,NA	NA|165aa|up_9|NZ_AP018033.1_2070326_2070821_+	pfam02577, DNase-RNase, Bifunctional nuclease	NA|226aa|up_8|NZ_AP018033.1_2071168_2071846_+	cd01105, HTH_GlnR-like, Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators	NA|942aa|up_7|NZ_AP018033.1_2072204_2075030_+	PRK05367, PRK05367, aminomethyl-transferring glycine dehydrogenase	NA|287aa|up_6|NZ_AP018033.1_2075256_2076117_-	PRK03204, PRK03204, haloalkane dehalogenase; Provisional	NA|289aa|up_5|NZ_AP018033.1_2076157_2077024_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|629aa|up_4|NZ_AP018033.1_2077028_2078915_-	TIGR00976, Hypothetical_protein_Rv1835c/MT1883/Mb1866c	NA|678aa|up_3|NZ_AP018033.1_2078930_2080964_-	cd01456, vWA_ywmD_type, VWA ywmD type:Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF)	NA|742aa|up_2|NZ_AP018033.1_2081083_2083309_-	PRK02999, PRK02999, malate synthase G; Provisional	NA|132aa|up_1|NZ_AP018033.1_2083584_2083980_-	COG1848, COG1848, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]	NA|88aa|up_0|NZ_AP018033.1_2083976_2084240_-	NA	NA|350aa|down_0|NZ_AP018033.1_2086008_2087058_-	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]	NA|456aa|down_1|NZ_AP018033.1_2087057_2088425_-	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]	NA|480aa|down_2|NZ_AP018033.1_2088598_2090038_-	PRK07807, PRK07807, GuaB1 family IMP dehydrogenase-related protein	NA|484aa|down_3|NZ_AP018033.1_2090070_2091522_-	PRK09287, PRK09287, NADP-dependent phosphogluconate dehydrogenase	NA|317aa|down_4|NZ_AP018033.1_2091551_2092502_-	cd07326, M56_BlaR1_MecR1_like, Peptidase M56-like including those in BlaR1 and MecR1, integral membrane metallopeptidase	NA|139aa|down_5|NZ_AP018033.1_2092516_2092933_-	COG3682, COG3682, Predicted transcriptional regulator [Transcription]	NA|141aa|down_6|NZ_AP018033.1_2093210_2093633_+	cd03443, PaaI_thioesterase, PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria	NA|101aa|down_7|NZ_AP018033.1_2093681_2093984_+	pfam00547, Urease_gamma, Urease, gamma subunit	NA|105aa|down_8|NZ_AP018033.1_2093980_2094295_+	PRK13202, ureB, urease subunit beta; Reviewed	NA|578aa|down_9|NZ_AP018033.1_2094294_2096028_+	PRK13206, ureC, urease subunit alpha; Reviewed
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	10	2166168-2166387	5	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	GTGCCAGCCGGAATCGTGATCGGCGGAACCGTCACCGACGGAATACTCA	49	0	0	NA	NA	NA	1	1	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|157aa|up_9|NZ_AP018033.1_2148845_2149316_-,NA|136aa|up_2|NZ_AP018033.1_2156340_2156748_-,NA	NA|157aa|up_9|NZ_AP018033.1_2148845_2149316_-	NA	NA|216aa|up_8|NZ_AP018033.1_2149655_2150303_-	pfam14081, DUF4262, Domain of unknown function (DUF4262)	NA|741aa|up_7|NZ_AP018033.1_2150309_2152532_-	PRK15061, PRK15061, catalase/peroxidase	NA|148aa|up_6|NZ_AP018033.1_2152569_2153013_-	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]	NA|198aa|up_5|NZ_AP018033.1_2153126_2153720_-	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|202aa|up_4|NZ_AP018033.1_2153802_2154408_-	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|251aa|up_3|NZ_AP018033.1_2155610_2156363_+	cd16282, metallo-hydrolase-like_MBL-fold, uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain	NA|136aa|up_2|NZ_AP018033.1_2156340_2156748_-	NA	NA|767aa|up_1|NZ_AP018033.1_2156882_2159183_+	PLN02892, PLN02892, isocitrate lyase	NA|1771aa|up_0|NZ_AP018033.1_2159352_2164665_-	pfam00823, PPE, PPE family	NA|155aa|down_0|NZ_AP018033.1_2168414_2168879_-	cd07821, PYR_PYL_RCAR_like, Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins	NA|288aa|down_1|NZ_AP018033.1_2168976_2169840_+	cd07987, LPLAT_MGAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: MGAT-like	NA|424aa|down_2|NZ_AP018033.1_2169877_2171149_-	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|372aa|down_3|NZ_AP018033.1_2171420_2172536_+	COG1680, AmpC, Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]	NA|447aa|down_4|NZ_AP018033.1_2172526_2173867_+	pfam00144, Beta-lactamase, Beta-lactamase	NA|621aa|down_5|NZ_AP018033.1_2174435_2176298_+	PRK12476, PRK12476, putative fatty-acid--CoA ligase; Provisional	NA|160aa|down_6|NZ_AP018033.1_2176305_2176785_-	pfam09167, DUF1942, Domain of unknown function (DUF1942)	NA|258aa|down_7|NZ_AP018033.1_2177021_2177795_+	COG3361, COG3361, Uncharacterized conserved protein [Function unknown]	NA|256aa|down_8|NZ_AP018033.1_2177798_2178566_-	PRK05867, PRK05867, SDR family oxidoreductase	NA|215aa|down_9|NZ_AP018033.1_2178610_2179255_-	TIGR03085, TIGR03085, TIGR03085 family protein
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	11	3107395-3109353	2,6,6	PILER-CR,CRISPRCasFinder,CRT	no	c2c9_V-U4,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type III-B,Type III-D,Type III-A,Type III-C	GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,NNNNNNNNGTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC	36,36,44	0	0	NA	NA	II-B,III-A:II-B,III-A:II-B,III-A	25,25,26	26	TypeIII-B,TypeIII-D,TypeIII-A,TypeIII-C	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|85aa|up_8|NZ_AP018033.1_3100674_3100929_-,NA|135aa|up_7|NZ_AP018033.1_3101076_3101481_+,NA|64aa|up_6|NZ_AP018033.1_3101477_3101669_+,NA|86aa|up_4|NZ_AP018033.1_3103255_3103513_+,NA|104aa|up_3|NZ_AP018033.1_3103617_3103929_+,NA|203aa|up_2|NZ_AP018033.1_3104348_3104957_+,NA	NA|92aa|up_9|NZ_AP018033.1_3100223_3100499_+	COG4453, COG4453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|85aa|up_8|NZ_AP018033.1_3100674_3100929_-	NA	NA|135aa|up_7|NZ_AP018033.1_3101076_3101481_+	NA	NA|64aa|up_6|NZ_AP018033.1_3101477_3101669_+	NA	NA|385aa|up_5|NZ_AP018033.1_3101867_3103022_+	pfam00665, rve, Integrase core domain	NA|86aa|up_4|NZ_AP018033.1_3103255_3103513_+	NA	NA|104aa|up_3|NZ_AP018033.1_3103617_3103929_+	NA	NA|203aa|up_2|NZ_AP018033.1_3104348_3104957_+	NA	NA|470aa|up_1|NZ_AP018033.1_3105027_3106437_+	pfam00665, rve, Integrase core domain	NA|271aa|up_0|NZ_AP018033.1_3106433_3107246_+	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	NA|421aa|down_0|NZ_AP018033.1_3109379_3110641_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas2|114aa|down_1|NZ_AP018033.1_3113255_3113597_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|339aa|down_2|NZ_AP018033.1_3113597_3114614_-	TIGR00287, CRISPR-associated_endonuclease_Cas1, CRISPR-associated endonuclease Cas1	csm6|383aa|down_3|NZ_AP018033.1_3114626_3115775_-	cd09699, Csm6_III-A, CRISPR/Cas system-associated protein Csm6	csm5gr7|376aa|down_4|NZ_AP018033.1_3115870_3116998_-	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm4gr5|303aa|down_5|NZ_AP018033.1_3116994_3117903_-	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm3gr7|237aa|down_6|NZ_AP018033.1_3117883_3118594_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|125aa|down_7|NZ_AP018033.1_3118603_3118978_-	TIGR01870, CRISPR_type_III-associated_protein_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2	cas10|813aa|down_8|NZ_AP018033.1_3118974_3121413_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|241aa|down_9|NZ_AP018033.1_3121409_3122132_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	12	3110676-3113207	7,7,3	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type III-B,Type III-D,Type III-A,Type III-C	GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGA	36,36,35	0	0	NA	NA	II-B,III-A:II-B,III-A:II-B,III-A	34,34,33	34	TypeIII-B,TypeIII-D,TypeIII-A,TypeIII-C	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|85aa|up_9|NZ_AP018033.1_3100674_3100929_-,NA|135aa|up_8|NZ_AP018033.1_3101076_3101481_+,NA|64aa|up_7|NZ_AP018033.1_3101477_3101669_+,NA|86aa|up_5|NZ_AP018033.1_3103255_3103513_+,NA|104aa|up_4|NZ_AP018033.1_3103617_3103929_+,NA|203aa|up_3|NZ_AP018033.1_3104348_3104957_+,NA	NA|85aa|up_9|NZ_AP018033.1_3100674_3100929_-	NA	NA|135aa|up_8|NZ_AP018033.1_3101076_3101481_+	NA	NA|64aa|up_7|NZ_AP018033.1_3101477_3101669_+	NA	NA|385aa|up_6|NZ_AP018033.1_3101867_3103022_+	pfam00665, rve, Integrase core domain	NA|86aa|up_5|NZ_AP018033.1_3103255_3103513_+	NA	NA|104aa|up_4|NZ_AP018033.1_3103617_3103929_+	NA	NA|203aa|up_3|NZ_AP018033.1_3104348_3104957_+	NA	NA|470aa|up_2|NZ_AP018033.1_3105027_3106437_+	pfam00665, rve, Integrase core domain	NA|271aa|up_1|NZ_AP018033.1_3106433_3107246_+	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	NA|421aa|up_0|NZ_AP018033.1_3109379_3110641_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas2|114aa|down_0|NZ_AP018033.1_3113255_3113597_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|339aa|down_1|NZ_AP018033.1_3113597_3114614_-	TIGR00287, CRISPR-associated_endonuclease_Cas1, CRISPR-associated endonuclease Cas1	csm6|383aa|down_2|NZ_AP018033.1_3114626_3115775_-	cd09699, Csm6_III-A, CRISPR/Cas system-associated protein Csm6	csm5gr7|376aa|down_3|NZ_AP018033.1_3115870_3116998_-	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm4gr5|303aa|down_4|NZ_AP018033.1_3116994_3117903_-	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm3gr7|237aa|down_5|NZ_AP018033.1_3117883_3118594_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|125aa|down_6|NZ_AP018033.1_3118603_3118978_-	TIGR01870, CRISPR_type_III-associated_protein_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2	cas10|813aa|down_7|NZ_AP018033.1_3118974_3121413_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|241aa|down_8|NZ_AP018033.1_3121409_3122132_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	NA|182aa|down_9|NZ_AP018033.1_3122531_3123077_-	COG4293, COG4293, Uncharacterized protein conserved in bacteria [Function unknown]
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	13	3835894-3835983	8	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	CCAGGCGTTGGGCTGGCTGCCGAT	24	0	0	NA	NA	NA	1	1	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|77aa|up_7|NZ_AP018033.1_3829288_3829519_+,NA|121aa|up_6|NZ_AP018033.1_3829622_3829985_-,NA|73aa|up_2|NZ_AP018033.1_3833959_3834178_-,NA|121aa|down_0|NZ_AP018033.1_3836968_3837331_-,NA|52aa|down_2|NZ_AP018033.1_3839172_3839328_-,NA|52aa|down_3|NZ_AP018033.1_3839352_3839508_-,NA|238aa|down_6|NZ_AP018033.1_3843543_3844257_-	NA|169aa|up_9|NZ_AP018033.1_3827599_3828106_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|409aa|up_8|NZ_AP018033.1_3828102_3829329_-	PRK00053, alr, alanine racemase; Reviewed	NA|77aa|up_7|NZ_AP018033.1_3829288_3829519_+	NA	NA|121aa|up_6|NZ_AP018033.1_3829622_3829985_-	NA	NA|177aa|up_5|NZ_AP018033.1_3830147_3830678_+	pfam00823, PPE, PPE family	NA|177aa|up_4|NZ_AP018033.1_3830944_3831475_+	pfam00823, PPE, PPE family	NA|725aa|up_3|NZ_AP018033.1_3831792_3833967_-	COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair]	NA|73aa|up_2|NZ_AP018033.1_3833959_3834178_-	NA	NA|100aa|up_1|NZ_AP018033.1_3834672_3834972_+	pfam00934, PE, PE family	NA|181aa|up_0|NZ_AP018033.1_3835057_3835600_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|121aa|down_0|NZ_AP018033.1_3836968_3837331_-	NA	NA|179aa|down_1|NZ_AP018033.1_3837493_3838030_+	pfam00823, PPE, PPE family	NA|52aa|down_2|NZ_AP018033.1_3839172_3839328_-	NA	NA|52aa|down_3|NZ_AP018033.1_3839352_3839508_-	NA	NA|461aa|down_4|NZ_AP018033.1_3840700_3842083_-	TIGR01788, Glutamate_decarboxylase_alpha_GAD-alpha	NA|474aa|down_5|NZ_AP018033.1_3842120_3843542_-	pfam01256, Carb_kinase, Carbohydrate kinase	NA|238aa|down_6|NZ_AP018033.1_3843543_3844257_-	NA	NA|285aa|down_7|NZ_AP018033.1_3844267_3845122_-	pfam14494, DUF4436, Domain of unknown function (DUF4436)	NA|625aa|down_8|NZ_AP018033.1_3845343_3847218_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|159aa|down_9|NZ_AP018033.1_3847239_3847716_+	pfam10708, DUF2510, Protein of unknown function (DUF2510)
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	14	3937687-3938849	8	CRT	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	CANCGGCGGCANCGGCGGCNCCGGCGGNNNCGGCGGCA	38	1	7	3938580-3938604|3938580-3938604|3938580-3938604|3938580-3938604|3938580-3938604|3938580-3938604|3938580-3938604	NZ_AP018033.1_675384-675360|NZ_AP018033.1_3726997-3726973|NZ_AP018033.1_3931117-3931141|NZ_AP018033.1_3931396-3931420|NZ_AP018033.1_3931804-3931828|NZ_AP018033.1_3932083-3932107|NZ_AP018033.1_4020356-4020332	NA	14	14	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA|280aa|down_2|NZ_AP018033.1_3942162_3943002_+	NA|318aa|up_9|NZ_AP018033.1_3910101_3911055_-	PRK07792, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional	NA|64aa|up_8|NZ_AP018033.1_3911079_3911271_-	COG1141, Fer, Ferredoxin [Energy production and conversion]	NA|401aa|up_7|NZ_AP018033.1_3911485_3912688_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|374aa|up_6|NZ_AP018033.1_3912712_3913834_+	COG1960, CaiA, Acyl-CoA dehydrogenases [Lipid metabolism]	NA|503aa|up_5|NZ_AP018033.1_3913904_3915413_+	PRK07867, PRK07867, acyl-CoA synthetase; Validated	NA|1438aa|up_4|NZ_AP018033.1_3915583_3919897_+	pfam00934, PE, PE family	NA|2127aa|up_3|NZ_AP018033.1_3920187_3926568_+	pfam00934, PE, PE family	NA|516aa|up_2|NZ_AP018033.1_3926734_3928282_-	PRK07586, PRK07586, acetolactate synthase large subunit	NA|279aa|up_1|NZ_AP018033.1_3928278_3929115_-	COG2159, COG2159, Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]	NA|219aa|up_0|NZ_AP018033.1_3935332_3935989_-	PRK07798, PRK07798, acyl-CoA synthetase; Validated	NA|549aa|down_0|NZ_AP018033.1_3939555_3941202_-	PRK07798, PRK07798, acyl-CoA synthetase; Validated	NA|264aa|down_1|NZ_AP018033.1_3941275_3942067_+	PRK07799, PRK07799, crotonase/enoyl-CoA hydratase family protein	NA|280aa|down_2|NZ_AP018033.1_3942162_3943002_+	NA	NA|399aa|down_3|NZ_AP018033.1_3943056_3944253_-	COG2124, CypX, Cytochrome P450 [Secondary metabolites biosynthesis, transport, and catabolism]	NA|237aa|down_4|NZ_AP018033.1_3944281_3944992_+	pfam06314, ADC, Acetoacetate decarboxylase (ADC)	NA|348aa|down_5|NZ_AP018033.1_3945056_3946100_-	TIGR03559, F420_Rv3520c, probable F420-dependent oxidoreductase, Rv3520c family	NA|304aa|down_6|NZ_AP018033.1_3946252_3947164_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|355aa|down_7|NZ_AP018033.1_3947179_3948244_+	PRK07937, PRK07937, lipid-transfer protein; Provisional	NA|395aa|down_8|NZ_AP018033.1_3948260_3949445_+	PRK08313, PRK08313, thiolase domain-containing protein	NA|344aa|down_9|NZ_AP018033.1_3949486_3950518_+	cd14952, NHL_PKND_like, NHL repeat domain of the protein kinase PknD
GCF_002356255.1_ASM235625v1	NZ_AP018033	Mycobacterium tuberculosis strain HN-024	15	4097379-4097467	9	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	GCTCGGCGACGATGCGGGCCGGATGACGGCC	31	0	0	NA	NA	NA	1	1	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm6,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|257aa|up_6|NZ_AP018033.1_4087965_4088736_-,NA|233aa|up_0|NZ_AP018033.1_4096483_4097182_-,NA|126aa|down_6|NZ_AP018033.1_4102702_4103080_+	NA|388aa|up_9|NZ_AP018033.1_4083636_4084800_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|351aa|up_8|NZ_AP018033.1_4084796_4085849_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|288aa|up_7|NZ_AP018033.1_4086347_4087211_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|257aa|up_6|NZ_AP018033.1_4087965_4088736_-	NA	NA|549aa|up_5|NZ_AP018033.1_4088732_4090379_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]	NA|288aa|up_4|NZ_AP018033.1_4090375_4091239_-	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|309aa|up_3|NZ_AP018033.1_4091231_4092158_-	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|542aa|up_2|NZ_AP018033.1_4092159_4093785_-	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|652aa|up_1|NZ_AP018033.1_4094492_4096448_+	PRK00174, PRK00174, acetyl-CoA synthetase; Provisional	NA|233aa|up_0|NZ_AP018033.1_4096483_4097182_-	NA	NA|173aa|down_0|NZ_AP018033.1_4097527_4098046_+	pfam07332, Phage_holin_3_6, Putative Actinobacterial Holin-X, holin superfamily III	NA|328aa|down_1|NZ_AP018033.1_4098046_4099030_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|398aa|down_2|NZ_AP018033.1_4099022_4100216_-	pfam13365, Trypsin_2, Trypsin-like peptidase domain	NA|274aa|down_3|NZ_AP018033.1_4100221_4101043_-	cd03426, CoAse, Coenzyme A pyrophosphatase (CoAse), a member of the Nudix hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes	NA|228aa|down_4|NZ_AP018033.1_4101174_4101858_-	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins	NA|246aa|down_5|NZ_AP018033.1_4101857_4102595_-	COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]	NA|126aa|down_6|NZ_AP018033.1_4102702_4103080_+	NA	NA|225aa|down_7|NZ_AP018033.1_4103178_4103853_+	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]	NA|265aa|down_8|NZ_AP018033.1_4103958_4104753_-	cd16278, metallo-hydrolase-like_MBL-fold, uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain	NA|152aa|down_9|NZ_AP018033.1_4104759_4105215_-	cd02199, YjgF_YER057c_UK114_like_1, This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function
