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_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	1	332008-332805	1	CRT	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,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,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA	NA|398aa|up_9|NZ_CP014566.1_321701_322895_-	COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]	NA|561aa|up_8|NZ_CP014566.1_322930_324613_+	PRK07788, PRK07788, acyl-CoA synthetase; Validated	NA|732aa|up_7|NZ_CP014566.1_324629_326825_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|378aa|up_6|NZ_CP014566.1_326938_328072_-	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|207aa|up_5|NZ_CP014566.1_328068_328689_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|194aa|up_4|NZ_CP014566.1_328785_329367_+	pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily	NA|242aa|up_3|NZ_CP014566.1_329296_330022_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|307aa|up_2|NZ_CP014566.1_330111_331032_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	NA|143aa|up_1|NZ_CP014566.1_331071_331500_-	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|86aa|up_0|NZ_CP014566.1_331523_331781_-	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|900aa|down_0|NZ_CP014566.1_334879_337579_-	pfam00934, PE, PE family	NA|835aa|down_1|NZ_CP014566.1_337828_340333_-	pfam00934, PE, PE family	NA|537aa|down_2|NZ_CP014566.1_340623_342234_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|303aa|down_3|NZ_CP014566.1_342257_343166_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|632aa|down_4|NZ_CP014566.1_343389_345285_+	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA	NA|539aa|down_5|NZ_CP014566.1_345281_346898_+	pfam05108, T7SS_ESX1_EccB, Type VII secretion system ESX-1, transport TM domain B	NA|1331aa|down_6|NZ_CP014566.1_346894_350887_+	TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa	NA|103aa|down_7|NZ_CP014566.1_350883_351192_+	pfam00934, PE, PE family	NA|514aa|down_8|NZ_CP014566.1_351194_352736_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|98aa|down_9|NZ_CP014566.1_352784_353078_+	TIGR03930, WXG100_ESAT6, WXG100 family type VII secretion target
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	2	693271-693347	1	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	TGAGGTGCGGCGTGAGCGCGGGT	23	0	0	NA	NA	NA	1	1	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA	NA|136aa|up_9|NZ_CP014566.1_679164_679572_+	cd18696, PIN_MtVapC26-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins	NA|229aa|up_8|NZ_CP014566.1_679631_680318_-	pfam10738, Lpp-LpqN, Probable lipoprotein LpqN	NA|878aa|up_7|NZ_CP014566.1_680471_683105_+	COG3537, COG3537, Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]	NA|796aa|up_6|NZ_CP014566.1_683127_685515_-	pfam03706, LPG_synthase_TM, Lysylphosphatidylglycerol synthase TM region	NA|241aa|up_5|NZ_CP014566.1_685652_686375_+	COG2186, FadR, Transcriptional regulators [Transcription]	NA|266aa|up_4|NZ_CP014566.1_686371_687169_+	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_CP014566.1_687170_688058_+	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_CP014566.1_688063_689278_+	pfam11887, Mce4_CUP1, Cholesterol uptake porter CUP1 of Mce4, putative	NA|344aa|up_1|NZ_CP014566.1_689274_690306_+	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_CP014566.1_690302_691748_+	TIGR00996, Mtu_fam_mce, virulence factor Mce family protein	NA|517aa|down_0|NZ_CP014566.1_694482_696033_+	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_CP014566.1_696084_696477_-	cd18768, PIN_MtVapC4-C5-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins	NA|86aa|down_2|NZ_CP014566.1_696473_696731_-	COG4118, Phd, Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]	NA|412aa|down_3|NZ_CP014566.1_696913_698149_-	COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General function prediction only]	NA|138aa|down_4|NZ_CP014566.1_698399_698813_-	cd18681, PIN_MtVapC27-VapC40_like, VapC-like PIN domain of Mycobacterium tuberculosis VapC27, and VapC40, and related proteins	NA|79aa|down_5|NZ_CP014566.1_698809_699046_-	COG2002, AbrB, Regulators of stationary/sporulation gene expression [Transcription]	NA|169aa|down_6|NZ_CP014566.1_699149_699656_-	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|157aa|down_7|NZ_CP014566.1_699769_700240_-	PRK10755, PRK10755, two-component system sensor histidine kinase PmrB	NA|254aa|down_8|NZ_CP014566.1_700283_701045_-	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_CP014566.1_701101_701413_+	pfam03413, PepSY, Peptidase propeptide and YPEB domain
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	3	928759-929670	2	CRT	no	csa3	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type I-A	CGGGGCCGGCGGGGCCGGCGG	21	1	23	929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652|929626-929652	NZ_CP014566.1_835329-835355|NZ_CP014566.1_331980-331954|NZ_CP014566.1_334994-334968|NZ_CP014566.1_337940-337914|NZ_CP014566.1_841580-841606|NZ_CP014566.1_842858-842884|NZ_CP014566.1_928492-928518|NZ_CP014566.1_2396468-2396442|NZ_CP014566.1_333216-333190|NZ_CP014566.1_335945-335919|NZ_CP014566.1_336284-336258|NZ_CP014566.1_339059-339033|NZ_CP014566.1_676371-676345|NZ_CP014566.1_838701-838727|NZ_CP014566.1_839799-839825|NZ_CP014566.1_928393-928419|NZ_CP014566.1_1216511-1216537|NZ_CP014566.1_1653681-1653655|NZ_CP014566.1_1842893-1842867|NZ_CP014566.1_2044373-2044347|NZ_CP014566.1_3787879-3787905|NZ_CP014566.1_3918131-3918157|NZ_CP014566.1_3918287-3918313	NA	19	19	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA|184aa|down_2|NZ_CP014566.1_933788_934340_-	NA|685aa|up_9|NZ_CP014566.1_916394_918449_-	TIGR00350, Transcriptional_regulator_LytR, cell envelope-related function transcriptional attenuator common domain	NA|390aa|up_8|NZ_CP014566.1_918614_919784_-	TIGR00737, Probable_tRNA-dihydrouridine_synthase, putative TIM-barrel protein, nifR3 family	NA|339aa|up_7|NZ_CP014566.1_919871_920888_-	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|214aa|up_6|NZ_CP014566.1_921049_921691_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|352aa|up_5|NZ_CP014566.1_921771_922827_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|131aa|up_4|NZ_CP014566.1_922878_923271_-	smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon Repressor	NA|141aa|up_3|NZ_CP014566.1_923328_923751_-	COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]	NA|97aa|up_2|NZ_CP014566.1_923712_924003_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|302aa|up_1|NZ_CP014566.1_924107_925013_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|272aa|up_0|NZ_CP014566.1_925031_925847_-	TIGR04255, hypothetical_protein, TIGR04255 family protein	NA|883aa|down_0|NZ_CP014566.1_930047_932696_-	pfam00934, PE, PE family	NA|215aa|down_1|NZ_CP014566.1_933163_933808_+	pfam14032, PknH_C, PknH-like extracellular domain	NA|184aa|down_2|NZ_CP014566.1_933788_934340_-	NA	NA|241aa|down_3|NZ_CP014566.1_934420_935143_-	COG4849, COG4849, Predicted nucleotidyltransferase [General function prediction    only]	NA|343aa|down_4|NZ_CP014566.1_935213_936242_-	COG4861, COG4861, Uncharacterized protein conserved in bacteria [Function unknown]	NA|261aa|down_5|NZ_CP014566.1_936930_937713_+	pfam01427, Peptidase_M15, D-ala-D-ala dipeptidase	NA|271aa|down_6|NZ_CP014566.1_937799_938612_+	pfam13847, Methyltransf_31, Methyltransferase domain	NA|287aa|down_7|NZ_CP014566.1_938679_939540_-	TIGR01250, Proline_iminopeptidase, proline-specific peptidase, Bacillus coagulans-type subfamily	NA|431aa|down_8|NZ_CP014566.1_940334_941627_+	cd17329, MFS_MdtH_MDR_like, Multidrug resistance protein MdtH and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|335aa|down_9|NZ_CP014566.1_941610_942615_+	COG1071, AcoA, Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	4	930607-930736	1	PILER-CR	no	csa3	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type I-A	CCGCCGGCTCCGCCGGTGGCGCCGC	25	0	0	NA	NA	NA	2	2	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA|184aa|down_1|NZ_CP014566.1_933788_934340_-	NA|390aa|up_9|NZ_CP014566.1_918614_919784_-	TIGR00737, Probable_tRNA-dihydrouridine_synthase, putative TIM-barrel protein, nifR3 family	NA|339aa|up_8|NZ_CP014566.1_919871_920888_-	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|214aa|up_7|NZ_CP014566.1_921049_921691_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|352aa|up_6|NZ_CP014566.1_921771_922827_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|131aa|up_5|NZ_CP014566.1_922878_923271_-	smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon Repressor	NA|141aa|up_4|NZ_CP014566.1_923328_923751_-	COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]	NA|97aa|up_3|NZ_CP014566.1_923712_924003_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|302aa|up_2|NZ_CP014566.1_924107_925013_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|272aa|up_1|NZ_CP014566.1_925031_925847_-	TIGR04255, hypothetical_protein, TIGR04255 family protein	NA|911aa|up_0|NZ_CP014566.1_927088_929821_+	pfam00934, PE, PE family	NA|215aa|down_0|NZ_CP014566.1_933163_933808_+	pfam14032, PknH_C, PknH-like extracellular domain	NA|184aa|down_1|NZ_CP014566.1_933788_934340_-	NA	NA|241aa|down_2|NZ_CP014566.1_934420_935143_-	COG4849, COG4849, Predicted nucleotidyltransferase [General function prediction    only]	NA|343aa|down_3|NZ_CP014566.1_935213_936242_-	COG4861, COG4861, Uncharacterized protein conserved in bacteria [Function unknown]	NA|261aa|down_4|NZ_CP014566.1_936930_937713_+	pfam01427, Peptidase_M15, D-ala-D-ala dipeptidase	NA|271aa|down_5|NZ_CP014566.1_937799_938612_+	pfam13847, Methyltransf_31, Methyltransferase domain	NA|287aa|down_6|NZ_CP014566.1_938679_939540_-	TIGR01250, Proline_iminopeptidase, proline-specific peptidase, Bacillus coagulans-type subfamily	NA|431aa|down_7|NZ_CP014566.1_940334_941627_+	cd17329, MFS_MdtH_MDR_like, Multidrug resistance protein MdtH and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily	NA|335aa|down_8|NZ_CP014566.1_941610_942615_+	COG1071, AcoA, Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]	NA|217aa|down_9|NZ_CP014566.1_942678_943329_-	COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	5	1214586-1215442	2	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	GGCGGTGTCGGCGGTGCCGGCGG	23	4	80	1214969-1214990|1214969-1214990|1215014-1215029|1215152-1215173|1215152-1215173|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287|1215269-1215287	NZ_CP014566.1_2917775-2917754|NZ_CP014566.1_2917841-2917820|NZ_CP014566.1_2071563-2071548|NZ_CP014566.1_839163-839184|NZ_CP014566.1_1220406-1220427|NZ_CP014566.1_335381-335363|NZ_CP014566.1_676035-676017|NZ_CP014566.1_841412-841430|NZ_CP014566.1_1220379-1220397|NZ_CP014566.1_1220451-1220469|NZ_CP014566.1_1628402-1628384|NZ_CP014566.1_1631228-1631210|NZ_CP014566.1_1634086-1634068|NZ_CP014566.1_1974200-1974182|NZ_CP014566.1_2044547-2044529|NZ_CP014566.1_2045093-2045075|NZ_CP014566.1_2758683-2758665|NZ_CP014566.1_2762203-2762185|NZ_CP014566.1_3910392-3910410|NZ_CP014566.1_150233-150251|NZ_CP014566.1_333372-333354|NZ_CP014566.1_336488-336470|NZ_CP014566.1_336941-336923|NZ_CP014566.1_336992-336974|NZ_CP014566.1_337001-336983|NZ_CP014566.1_339272-339254|NZ_CP014566.1_339392-339374|NZ_CP014566.1_339659-339641|NZ_CP014566.1_339688-339706|NZ_CP014566.1_339782-339764|NZ_CP014566.1_364358-364340|NZ_CP014566.1_444573-444555|NZ_CP014566.1_547917-547899|NZ_CP014566.1_625226-625244|NZ_CP014566.1_625448-625466|NZ_CP014566.1_675201-675183|NZ_CP014566.1_842360-842378|NZ_CP014566.1_1093118-1093136|NZ_CP014566.1_1093766-1093784|NZ_CP014566.1_1097836-1097818|NZ_CP014566.1_1215641-1215659|NZ_CP014566.1_1216148-1216166|NZ_CP014566.1_1216400-1216418|NZ_CP014566.1_1216418-1216436|NZ_CP014566.1_1220799-1220817|NZ_CP014566.1_1488609-1488591|NZ_CP014566.1_1616354-1616336|NZ_CP014566.1_1616807-1616789|NZ_CP014566.1_1633951-1633933|NZ_CP014566.1_1633960-1633942|NZ_CP014566.1_1634173-1634155|NZ_CP014566.1_1634224-1634206|NZ_CP014566.1_1842470-1842452|NZ_CP014566.1_1842998-1842980|NZ_CP014566.1_1973474-1973456|NZ_CP014566.1_1984435-1984453|NZ_CP014566.1_2071761-2071743|NZ_CP014566.1_2279939-2279921|NZ_CP014566.1_2331189-2331171|NZ_CP014566.1_2392398-2392416|NZ_CP014566.1_2396381-2396363|NZ_CP014566.1_2539064-2539046|NZ_CP014566.1_2651341-2651359|NZ_CP014566.1_2751999-2751981|NZ_CP014566.1_2752581-2752563|NZ_CP014566.1_3001051-3001069|NZ_CP014566.1_3001150-3001168|NZ_CP014566.1_3691981-3691999|NZ_CP014566.1_3723131-3723113|NZ_CP014566.1_3723755-3723737|NZ_CP014566.1_3723998-3723980|NZ_CP014566.1_3724130-3724112|NZ_CP014566.1_3726035-3726017|NZ_CP014566.1_3786460-3786478|NZ_CP014566.1_3786643-3786661|NZ_CP014566.1_3907825-3907843|NZ_CP014566.1_3909564-3909582|NZ_CP014566.1_3910218-3910236|NZ_CP014566.1_3918509-3918527|NZ_CP014566.1_4007980-4007962	NA	16	16	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|89aa|up_3|NZ_CP014566.1_1210018_1210285_+,NA|61aa|down_3|NZ_CP014566.1_1217986_1218169_+	NA|465aa|up_9|NZ_CP014566.1_1204352_1205747_+	TIGR01137, Cystathionine_beta-synthase, cystathionine beta-synthase	NA|241aa|up_8|NZ_CP014566.1_1205948_1206671_+	pfam06271, RDD, RDD family	NA|389aa|up_7|NZ_CP014566.1_1206702_1207869_+	PRK07811, PRK07811, cystathionine gamma-synthase; Provisional	NA|165aa|up_6|NZ_CP014566.1_1207939_1208434_-	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|145aa|up_5|NZ_CP014566.1_1208619_1209054_-	pfam14155, DUF4307, Domain of unknown function (DUF4307)	NA|289aa|up_4|NZ_CP014566.1_1209155_1210022_+	TIGR03446, mycothiol_Mca, mycothiol conjugate amidase Mca	NA|89aa|up_3|NZ_CP014566.1_1210018_1210285_+	NA	NA|674aa|up_2|NZ_CP014566.1_1210271_1212293_+	COG1331, COG1331, Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]	NA|243aa|up_1|NZ_CP014566.1_1212391_1213120_-	TIGR01065, Hypothetical_UPF0073_protein_yqfA	NA|263aa|up_0|NZ_CP014566.1_1213230_1214019_+	PRK14828, PRK14828, undecaprenyl pyrophosphate synthase; Provisional	NA|107aa|down_0|NZ_CP014566.1_1216801_1217122_+	COG0020, UppS, Undecaprenyl pyrophosphate synthase [Lipid metabolism]	NA|145aa|down_1|NZ_CP014566.1_1217274_1217709_+	pfam00934, PE, PE family	NA|55aa|down_2|NZ_CP014566.1_1217810_1217975_+	smart00637, CBD_II, CBD_II domain	NA|61aa|down_3|NZ_CP014566.1_1217986_1218169_+	NA	NA|152aa|down_4|NZ_CP014566.1_1218360_1218816_+	pfam01670, Glyco_hydro_12, Glycosyl hydrolase family 12	NA|851aa|down_5|NZ_CP014566.1_1219230_1221783_+	pfam00934, PE, PE family	NA|313aa|down_6|NZ_CP014566.1_1222000_1222939_-	PRK05439, PRK05439, pantothenate kinase; Provisional	NA|427aa|down_7|NZ_CP014566.1_1223326_1224607_+	PRK00011, glyA, serine hydroxymethyltransferase; Reviewed	NA|276aa|down_8|NZ_CP014566.1_1224711_1225539_+	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|434aa|down_9|NZ_CP014566.1_1225749_1227051_+	COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family domains [General    function prediction only]
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	6	1634721-1634958	2	PILER-CR	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	CGTTGGCGCCGTTGCCGCCGGCACCGCCGTCGCCGCCG	38	0	0	NA	NA	NA	2	2	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|80aa|up_9|NZ_CP014566.1_1620459_1620699_+,NA|38aa|up_8|NZ_CP014566.1_1620827_1620941_-,NA|137aa|up_7|NZ_CP014566.1_1620990_1621401_-,NA|288aa|down_2|NZ_CP014566.1_1638590_1639454_+	NA|80aa|up_9|NZ_CP014566.1_1620459_1620699_+	NA	NA|38aa|up_8|NZ_CP014566.1_1620827_1620941_-	NA	NA|137aa|up_7|NZ_CP014566.1_1620990_1621401_-	NA	NA|248aa|up_6|NZ_CP014566.1_1621417_1622161_-	pfam01182, Glucosamine_iso, Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase	NA|304aa|up_5|NZ_CP014566.1_1622157_1623069_-	TIGR00534, Putative_OxPP_cycle_protein_OpcA, glucose-6-phosphate dehydrogenase assembly protein OpcA	NA|515aa|up_4|NZ_CP014566.1_1623121_1624666_-	PRK05722, PRK05722, glucose-6-phosphate 1-dehydrogenase; Validated	NA|374aa|up_3|NZ_CP014566.1_1624662_1625784_-	PRK03343, PRK03343, transaldolase; Validated	NA|701aa|up_2|NZ_CP014566.1_1625800_1627903_-	COG0021, TktA, Transketolase [Carbohydrate transport and metabolism]	NA|1400aa|up_1|NZ_CP014566.1_1628341_1632541_-	pfam00934, PE, PE family	NA|309aa|up_0|NZ_CP014566.1_1632942_1633869_+	PRK04375, PRK04375, protoheme IX farnesyltransferase; Provisional	NA|422aa|down_0|NZ_CP014566.1_1636291_1637557_+	COG2508, COG2508, Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]	NA|329aa|down_1|NZ_CP014566.1_1637584_1638571_-	cd05286, QOR2, Quinone oxidoreductase (QOR)	NA|288aa|down_2|NZ_CP014566.1_1638590_1639454_+	NA	NA|311aa|down_3|NZ_CP014566.1_1639403_1640336_-	COG1612, CtaA, Uncharacterized protein required for cytochrome oxidase assembly [Posttranslational modification, protein turnover, chaperones]	NA|262aa|down_4|NZ_CP014566.1_1640447_1641233_-	TIGR00025, Mtu_efflux, ABC transporter efflux protein, DrrB family	NA|314aa|down_5|NZ_CP014566.1_1641229_1642171_-	COG1131, CcmA, ABC-type multidrug transport system, ATPase component [Defense mechanisms]	NA|592aa|down_6|NZ_CP014566.1_1642326_1644102_-	TIGR03459, crt_membr, carotene biosynthesis associated membrane protein	NA|269aa|down_7|NZ_CP014566.1_1644149_1644956_+	COG2345, COG2345, Predicted transcriptional regulator [Transcription]	NA|847aa|down_8|NZ_CP014566.1_1644952_1647493_+	TIGR01980, UPF0051_protein_slr0074, FeS assembly protein SufB	NA|398aa|down_9|NZ_CP014566.1_1647489_1648683_+	COG0719, SufB, Cysteine desulfurase activator SufB [Posttranslational modification, protein turnover, chaperones]
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	7	2071233-2071487	3	CRT	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	GCCNCCGTCGCCGCCNNTGCC	21	2	3	2071314-2071331|2071314-2071331|2071404-2071421	NZ_CP014566.1_402340-402323|NZ_CP014566.1_608588-608571|NZ_CP014566.1_3397351-3397334	NA	5	5	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|88aa|up_0|NZ_CP014566.1_2070592_2070856_-,NA	NA|165aa|up_9|NZ_CP014566.1_2056942_2057437_+	pfam02577, DNase-RNase, Bifunctional nuclease	NA|226aa|up_8|NZ_CP014566.1_2057784_2058462_+	cd01105, HTH_GlnR-like, Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators	NA|942aa|up_7|NZ_CP014566.1_2058820_2061646_+	PRK05367, PRK05367, aminomethyl-transferring glycine dehydrogenase	NA|287aa|up_6|NZ_CP014566.1_2061872_2062733_-	PRK03204, PRK03204, haloalkane dehalogenase; Provisional	NA|289aa|up_5|NZ_CP014566.1_2062773_2063640_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|629aa|up_4|NZ_CP014566.1_2063644_2065531_-	TIGR00976, Hypothetical_protein_Rv1835c/MT1883/Mb1866c	NA|678aa|up_3|NZ_CP014566.1_2065546_2067580_-	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_CP014566.1_2067699_2069925_-	PRK02999, PRK02999, malate synthase G; Provisional	NA|132aa|up_1|NZ_CP014566.1_2070200_2070596_-	COG1848, COG1848, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]	NA|88aa|up_0|NZ_CP014566.1_2070592_2070856_-	NA	NA|350aa|down_0|NZ_CP014566.1_2072623_2073673_-	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]	NA|456aa|down_1|NZ_CP014566.1_2073672_2075040_-	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]	NA|480aa|down_2|NZ_CP014566.1_2075213_2076653_-	PRK07807, PRK07807, GuaB1 family IMP dehydrogenase-related protein	NA|317aa|down_3|NZ_CP014566.1_2078165_2079116_-	cd07326, M56_BlaR1_MecR1_like, Peptidase M56-like including those in BlaR1 and MecR1, integral membrane metallopeptidase	NA|139aa|down_4|NZ_CP014566.1_2079130_2079547_-	COG3682, COG3682, Predicted transcriptional regulator [Transcription]	NA|141aa|down_5|NZ_CP014566.1_2079824_2080247_+	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_6|NZ_CP014566.1_2080295_2080598_+	pfam00547, Urease_gamma, Urease, gamma subunit	NA|105aa|down_7|NZ_CP014566.1_2080594_2080909_+	PRK13202, ureB, urease subunit beta; Reviewed	NA|578aa|down_8|NZ_CP014566.1_2080908_2082642_+	PRK13206, ureC, urease subunit alpha; Reviewed	NA|212aa|down_9|NZ_CP014566.1_2082641_2083277_+	COG0830, UreF, Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	8	2152964-2153089	3	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	TGCCAGCCGGAATCGTGATCGGCGGAACCGTCACCGACGGAATACTCA	48	0	0	NA	NA	NA	1	1	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|136aa|up_2|NZ_CP014566.1_2142939_2143347_-,NA|127aa|down_5|NZ_CP014566.1_2160698_2161079_-	NA|216aa|up_9|NZ_CP014566.1_2136253_2136901_-	pfam14081, DUF4262, Domain of unknown function (DUF4262)	NA|741aa|up_8|NZ_CP014566.1_2136907_2139130_-	PRK15061, PRK15061, catalase/peroxidase	NA|148aa|up_7|NZ_CP014566.1_2139167_2139611_-	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]	NA|198aa|up_6|NZ_CP014566.1_2139724_2140318_-	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|202aa|up_5|NZ_CP014566.1_2140400_2141006_-	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|335aa|up_4|NZ_CP014566.1_2141105_2142110_-	cd08275, MDR3, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family	NA|251aa|up_3|NZ_CP014566.1_2142209_2142962_+	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_CP014566.1_2142939_2143347_-	NA	NA|767aa|up_1|NZ_CP014566.1_2143481_2145782_+	PLN02892, PLN02892, isocitrate lyase	NA|1836aa|up_0|NZ_CP014566.1_2145951_2151459_-	pfam00823, PPE, PPE family	NA|155aa|down_0|NZ_CP014566.1_2155209_2155674_-	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_CP014566.1_2155771_2156635_+	cd07987, LPLAT_MGAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: MGAT-like	NA|424aa|down_2|NZ_CP014566.1_2156672_2157944_-	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|372aa|down_3|NZ_CP014566.1_2158215_2159331_+	COG1680, AmpC, Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]	NA|447aa|down_4|NZ_CP014566.1_2159321_2160662_+	pfam00144, Beta-lactamase, Beta-lactamase	NA|127aa|down_5|NZ_CP014566.1_2160698_2161079_-	NA	NA|621aa|down_6|NZ_CP014566.1_2161235_2163098_+	PRK12476, PRK12476, putative fatty-acid--CoA ligase; Provisional	NA|160aa|down_7|NZ_CP014566.1_2163105_2163585_-	pfam09167, DUF1942, Domain of unknown function (DUF1942)	NA|258aa|down_8|NZ_CP014566.1_2163821_2164595_+	COG3361, COG3361, Uncharacterized conserved protein [Function unknown]	NA|256aa|down_9|NZ_CP014566.1_2164598_2165366_-	PRK05867, PRK05867, SDR family oxidoreductase
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	9	3065406-3066833	3,4,4,4	PILER-CR,CRISPRCasFinder,CRT,PILER-CR	no	c2c9_V-U4,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type III-A,Type III-B,Type III-C,Type III-D	GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC	36,36,36,36	0	0	NA	NA	II-B,III-A:II-B,III-A:II-B,III-A:II-B,III-A	15,18,19,15	19	TypeIII-A,TypeIII-B,TypeIII-C,TypeIII-D	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|85aa|up_8|NZ_CP014566.1_3058685_3058940_-,NA|135aa|up_7|NZ_CP014566.1_3059087_3059492_+,NA|64aa|up_6|NZ_CP014566.1_3059488_3059680_+,NA|86aa|up_4|NZ_CP014566.1_3061266_3061524_+,NA|104aa|up_3|NZ_CP014566.1_3061628_3061940_+,NA|203aa|up_2|NZ_CP014566.1_3062359_3062968_+,NA	NA|92aa|up_9|NZ_CP014566.1_3058234_3058510_+	COG4453, COG4453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|85aa|up_8|NZ_CP014566.1_3058685_3058940_-	NA	NA|135aa|up_7|NZ_CP014566.1_3059087_3059492_+	NA	NA|64aa|up_6|NZ_CP014566.1_3059488_3059680_+	NA	NA|385aa|up_5|NZ_CP014566.1_3059878_3061033_+	pfam00665, rve, Integrase core domain	NA|86aa|up_4|NZ_CP014566.1_3061266_3061524_+	NA	NA|104aa|up_3|NZ_CP014566.1_3061628_3061940_+	NA	NA|203aa|up_2|NZ_CP014566.1_3062359_3062968_+	NA	NA|470aa|up_1|NZ_CP014566.1_3063038_3064448_+	pfam00665, rve, Integrase core domain	NA|271aa|up_0|NZ_CP014566.1_3064444_3065257_+	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	NA|421aa|down_0|NZ_CP014566.1_3066859_3068121_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas2|114aa|down_1|NZ_CP014566.1_3070374_3070716_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|339aa|down_2|NZ_CP014566.1_3070716_3071733_-	TIGR00287, CRISPR-associated_endonuclease_Cas1, CRISPR-associated endonuclease Cas1	csm5gr7|376aa|down_3|NZ_CP014566.1_3072989_3074117_-	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm4gr5|303aa|down_4|NZ_CP014566.1_3074113_3075022_-	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm3gr7|237aa|down_5|NZ_CP014566.1_3075002_3075713_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|125aa|down_6|NZ_CP014566.1_3075722_3076097_-	TIGR01870, CRISPR_type_III-associated_protein_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2	cas10|813aa|down_7|NZ_CP014566.1_3076093_3078532_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|241aa|down_8|NZ_CP014566.1_3078528_3079251_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	NA|182aa|down_9|NZ_CP014566.1_3079650_3080196_-	COG4293, COG4293, Uncharacterized protein conserved in bacteria [Function unknown]
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	10	3068156-3070326	5,5,5	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type III-A,Type III-B,Type III-C,Type III-D	GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC	36,36,36	0	0	NA	NA	II-B,III-A:II-B,III-A:II-B,III-A	29,29,28	29	TypeIII-A,TypeIII-B,TypeIII-C,TypeIII-D	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|85aa|up_9|NZ_CP014566.1_3058685_3058940_-,NA|135aa|up_8|NZ_CP014566.1_3059087_3059492_+,NA|64aa|up_7|NZ_CP014566.1_3059488_3059680_+,NA|86aa|up_5|NZ_CP014566.1_3061266_3061524_+,NA|104aa|up_4|NZ_CP014566.1_3061628_3061940_+,NA|203aa|up_3|NZ_CP014566.1_3062359_3062968_+,NA	NA|85aa|up_9|NZ_CP014566.1_3058685_3058940_-	NA	NA|135aa|up_8|NZ_CP014566.1_3059087_3059492_+	NA	NA|64aa|up_7|NZ_CP014566.1_3059488_3059680_+	NA	NA|385aa|up_6|NZ_CP014566.1_3059878_3061033_+	pfam00665, rve, Integrase core domain	NA|86aa|up_5|NZ_CP014566.1_3061266_3061524_+	NA	NA|104aa|up_4|NZ_CP014566.1_3061628_3061940_+	NA	NA|203aa|up_3|NZ_CP014566.1_3062359_3062968_+	NA	NA|470aa|up_2|NZ_CP014566.1_3063038_3064448_+	pfam00665, rve, Integrase core domain	NA|271aa|up_1|NZ_CP014566.1_3064444_3065257_+	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	NA|421aa|up_0|NZ_CP014566.1_3066859_3068121_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas2|114aa|down_0|NZ_CP014566.1_3070374_3070716_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|339aa|down_1|NZ_CP014566.1_3070716_3071733_-	TIGR00287, CRISPR-associated_endonuclease_Cas1, CRISPR-associated endonuclease Cas1	csm5gr7|376aa|down_2|NZ_CP014566.1_3072989_3074117_-	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm4gr5|303aa|down_3|NZ_CP014566.1_3074113_3075022_-	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm3gr7|237aa|down_4|NZ_CP014566.1_3075002_3075713_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|125aa|down_5|NZ_CP014566.1_3075722_3076097_-	TIGR01870, CRISPR_type_III-associated_protein_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2	cas10|813aa|down_6|NZ_CP014566.1_3076093_3078532_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|241aa|down_7|NZ_CP014566.1_3078528_3079251_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	NA|182aa|down_8|NZ_CP014566.1_3079650_3080196_-	COG4293, COG4293, Uncharacterized protein conserved in bacteria [Function unknown]	NA|295aa|down_9|NZ_CP014566.1_3080467_3081352_-	COG2253, COG2253, Uncharacterized conserved protein [Function unknown]
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	11	3747955-3748081	6	PILER-CR	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	GTTGCCGATGCCGGTGTTGAAA	22	0	0	NA	NA	NA	2	2	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|96aa|up_1|NZ_CP014566.1_3740800_3741088_-,NA|87aa|down_4|NZ_CP014566.1_3754201_3754462_-	NA|450aa|up_9|NZ_CP014566.1_3715321_3716671_+	PRK07812, PRK07812, O-acetylhomoserine aminocarboxypropyltransferase; Validated	NA|380aa|up_8|NZ_CP014566.1_3716682_3717822_+	PRK00175, metX, homoserine O-acetyltransferase; Provisional	NA|244aa|up_7|NZ_CP014566.1_3717818_3718550_+	pfam08241, Methyltransf_11, Methyltransferase domain	NA|1339aa|up_6|NZ_CP014566.1_3718558_3722575_-	pfam00823, PPE, PPE family	NA|1875aa|up_5|NZ_CP014566.1_3722623_3728248_-	pfam00934, PE, PE family	NA|86aa|up_4|NZ_CP014566.1_3728677_3728935_-	pfam11222, DUF3017, Protein of unknown function (DUF3017)	NA|149aa|up_3|NZ_CP014566.1_3739287_3739734_+	pfam01548, DEDD_Tnp_IS110, Transposase	NA|247aa|up_2|NZ_CP014566.1_3739770_3740511_-	pfam01610, DDE_Tnp_ISL3, Transposase	NA|96aa|up_1|NZ_CP014566.1_3740800_3741088_-	NA	NA|1445aa|up_0|NZ_CP014566.1_3741424_3745759_-	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|433aa|down_0|NZ_CP014566.1_3751269_3752568_-	pfam00823, PPE, PPE family	NA|265aa|down_1|NZ_CP014566.1_3752811_3753606_-	pfam08031, BBE, Berberine and berberine like	NA|124aa|down_2|NZ_CP014566.1_3753687_3754059_-	COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion]	NA|73aa|down_3|NZ_CP014566.1_3753956_3754175_-	pfam01565, FAD_binding_4, FAD binding domain	NA|87aa|down_4|NZ_CP014566.1_3754201_3754462_-	NA	NA|130aa|down_5|NZ_CP014566.1_3754576_3754966_+	pfam05305, DUF732, Protein of unknown function (DUF732)	NA|98aa|down_6|NZ_CP014566.1_3754979_3755273_-	pfam11222, DUF3017, Protein of unknown function (DUF3017)	NA|282aa|down_7|NZ_CP014566.1_3755269_3756115_-	PRK14193, PRK14193, bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional	NA|92aa|down_8|NZ_CP014566.1_3756238_3756514_+	COG2161, StbD, Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]	NA|86aa|down_9|NZ_CP014566.1_3756510_3756768_+	pfam06769, YoeB_toxin, YoeB-like toxin of bacterial type II toxin-antitoxin system
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	12	4064375-4064700	6	CRISPRCasFinder	no	cas3	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Unclear	CGCCGGGCTGTTCGGCGACGGCGGC	25	1	36	4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421|4064400-4064421	NZ_CP014566.1_971965-971944|NZ_CP014566.1_339391-339370|NZ_CP014566.1_1842571-1842550|NZ_CP014566.1_2396839-2396818|NZ_CP014566.1_3723130-3723109|NZ_CP014566.1_3923669-3923690|NZ_CP014566.1_335194-335173|NZ_CP014566.1_335380-335359|NZ_CP014566.1_336487-336466|NZ_CP014566.1_336991-336970|NZ_CP014566.1_339085-339064|NZ_CP014566.1_673751-673730|NZ_CP014566.1_675200-675179|NZ_CP014566.1_841260-841281|NZ_CP014566.1_930545-930524|NZ_CP014566.1_971485-971464|NZ_CP014566.1_1093119-1093140|NZ_CP014566.1_1192078-1192057|NZ_CP014566.1_1194280-1194259|NZ_CP014566.1_1488608-1488587|NZ_CP014566.1_1973620-1973599|NZ_CP014566.1_1974850-1974829|NZ_CP014566.1_1985225-1985246|NZ_CP014566.1_2044900-2044879|NZ_CP014566.1_2761178-2761157|NZ_CP014566.1_3109534-3109555|NZ_CP014566.1_3726034-3726013|NZ_CP014566.1_3764559-3764580|NZ_CP014566.1_3911980-3912001|NZ_CP014566.1_3912304-3912325|NZ_CP014566.1_3912901-3912922|NZ_CP014566.1_3913525-3913546|NZ_CP014566.1_3918576-3918597|NZ_CP014566.1_3920670-3920691|NZ_CP014566.1_4007880-4007859|NZ_CP014566.1_4007979-4007958	NA	5	5	Unclear	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|193aa|up_6|NZ_CP014566.1_4057877_4058456_-,NA|52aa|up_1|NZ_CP014566.1_4063288_4063444_-,NA|100aa|down_1|NZ_CP014566.1_4065359_4065659_-,NA|257aa|down_8|NZ_CP014566.1_4071624_4072395_-	NA|402aa|up_9|NZ_CP014566.1_4051783_4052989_-	PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated	NA|550aa|up_8|NZ_CP014566.1_4053074_4054724_+	cd07302, CHD, cyclase homology domain	NA|935aa|up_7|NZ_CP014566.1_4054720_4057525_-	PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated	NA|193aa|up_6|NZ_CP014566.1_4057877_4058456_-	NA	NA|68aa|up_5|NZ_CP014566.1_4058595_4058799_-	COG1278, CspC, Cold shock proteins [Transcription]	cas3|772aa|up_4|NZ_CP014566.1_4059048_4061364_+	TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase	NA|95aa|up_3|NZ_CP014566.1_4061500_4061785_+	pfam00934, PE, PE family	NA|346aa|up_2|NZ_CP014566.1_4062108_4063146_+	pfam18621, DUF5628, Family of unknown function (DUF5628)	NA|52aa|up_1|NZ_CP014566.1_4063288_4063444_-	NA	NA|105aa|up_0|NZ_CP014566.1_4063899_4064214_+	pfam00934, PE, PE family	NA|126aa|down_0|NZ_CP014566.1_4065019_4065397_-	TIGR03816, tadE_like_DECH, helicase/secretion neighborhood TadE-like protein	NA|100aa|down_1|NZ_CP014566.1_4065359_4065659_-	NA	NA|69aa|down_2|NZ_CP014566.1_4065682_4065889_-	pfam14029, DUF4244, Protein of unknown function (DUF4244)	NA|192aa|down_3|NZ_CP014566.1_4065898_4066474_-	COG2064, TadC, Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]	NA|267aa|down_4|NZ_CP014566.1_4066497_4067298_-	COG4965, TadB, Flp pilus assembly protein TadB [Intracellular trafficking and secretion]	NA|388aa|down_5|NZ_CP014566.1_4067294_4068458_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|351aa|down_6|NZ_CP014566.1_4068454_4069507_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|288aa|down_7|NZ_CP014566.1_4070006_4070870_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|257aa|down_8|NZ_CP014566.1_4071624_4072395_-	NA	NA|549aa|down_9|NZ_CP014566.1_4072391_4074038_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	13	4064777-4064855	7	CRISPRCasFinder	no	cas3	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Unclear	CGCCGGGCTGTTCGGCGACGGCGGC	25	0	0	NA	NA	NA	1	1	Unclear	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|193aa|up_6|NZ_CP014566.1_4057877_4058456_-,NA|52aa|up_1|NZ_CP014566.1_4063288_4063444_-,NA|100aa|down_1|NZ_CP014566.1_4065359_4065659_-,NA|257aa|down_8|NZ_CP014566.1_4071624_4072395_-	NA|402aa|up_9|NZ_CP014566.1_4051783_4052989_-	PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated	NA|550aa|up_8|NZ_CP014566.1_4053074_4054724_+	cd07302, CHD, cyclase homology domain	NA|935aa|up_7|NZ_CP014566.1_4054720_4057525_-	PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated	NA|193aa|up_6|NZ_CP014566.1_4057877_4058456_-	NA	NA|68aa|up_5|NZ_CP014566.1_4058595_4058799_-	COG1278, CspC, Cold shock proteins [Transcription]	cas3|772aa|up_4|NZ_CP014566.1_4059048_4061364_+	TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase	NA|95aa|up_3|NZ_CP014566.1_4061500_4061785_+	pfam00934, PE, PE family	NA|346aa|up_2|NZ_CP014566.1_4062108_4063146_+	pfam18621, DUF5628, Family of unknown function (DUF5628)	NA|52aa|up_1|NZ_CP014566.1_4063288_4063444_-	NA	NA|105aa|up_0|NZ_CP014566.1_4063899_4064214_+	pfam00934, PE, PE family	NA|126aa|down_0|NZ_CP014566.1_4065019_4065397_-	TIGR03816, tadE_like_DECH, helicase/secretion neighborhood TadE-like protein	NA|100aa|down_1|NZ_CP014566.1_4065359_4065659_-	NA	NA|69aa|down_2|NZ_CP014566.1_4065682_4065889_-	pfam14029, DUF4244, Protein of unknown function (DUF4244)	NA|192aa|down_3|NZ_CP014566.1_4065898_4066474_-	COG2064, TadC, Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]	NA|267aa|down_4|NZ_CP014566.1_4066497_4067298_-	COG4965, TadB, Flp pilus assembly protein TadB [Intracellular trafficking and secretion]	NA|388aa|down_5|NZ_CP014566.1_4067294_4068458_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|351aa|down_6|NZ_CP014566.1_4068454_4069507_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|288aa|down_7|NZ_CP014566.1_4070006_4070870_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|257aa|down_8|NZ_CP014566.1_4071624_4072395_-	NA	NA|549aa|down_9|NZ_CP014566.1_4072391_4074038_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]
GCF_001580385.1_ASM158038v1	NZ_CP014566	Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172 chromosome, complete genome	14	4081037-4081125	8	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,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,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|257aa|up_5|NZ_CP014566.1_4071624_4072395_-,NA|233aa|up_0|NZ_CP014566.1_4080141_4080840_-,NA|126aa|down_6|NZ_CP014566.1_4086360_4086738_+	NA|267aa|up_9|NZ_CP014566.1_4066497_4067298_-	COG4965, TadB, Flp pilus assembly protein TadB [Intracellular trafficking and secretion]	NA|388aa|up_8|NZ_CP014566.1_4067294_4068458_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|351aa|up_7|NZ_CP014566.1_4068454_4069507_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|288aa|up_6|NZ_CP014566.1_4070006_4070870_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|257aa|up_5|NZ_CP014566.1_4071624_4072395_-	NA	NA|549aa|up_4|NZ_CP014566.1_4072391_4074038_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]	NA|288aa|up_3|NZ_CP014566.1_4074034_4074898_-	COG1173, DppC, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|309aa|up_2|NZ_CP014566.1_4074890_4075817_-	COG0601, DppB, ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]	NA|542aa|up_1|NZ_CP014566.1_4075818_4077444_-	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|233aa|up_0|NZ_CP014566.1_4080141_4080840_-	NA	NA|173aa|down_0|NZ_CP014566.1_4081185_4081704_+	pfam07332, Phage_holin_3_6, Putative Actinobacterial Holin-X, holin superfamily III	NA|328aa|down_1|NZ_CP014566.1_4081704_4082688_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|398aa|down_2|NZ_CP014566.1_4082680_4083874_-	pfam13365, Trypsin_2, Trypsin-like peptidase domain	NA|274aa|down_3|NZ_CP014566.1_4083879_4084701_-	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_CP014566.1_4084832_4085516_-	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins	NA|246aa|down_5|NZ_CP014566.1_4085515_4086253_-	COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]	NA|126aa|down_6|NZ_CP014566.1_4086360_4086738_+	NA	NA|225aa|down_7|NZ_CP014566.1_4086836_4087511_+	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]	NA|265aa|down_8|NZ_CP014566.1_4087616_4088411_-	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_CP014566.1_4088417_4088873_-	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
