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_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	1	332002-332799	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_AM412059.1_321695_322889_-	COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]	NA|561aa|up_8|NZ_AM412059.1_322924_324607_+	PRK07788, PRK07788, acyl-CoA synthetase; Validated	NA|732aa|up_7|NZ_AM412059.1_324623_326819_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|378aa|up_6|NZ_AM412059.1_326932_328066_-	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|207aa|up_5|NZ_AM412059.1_328062_328683_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|194aa|up_4|NZ_AM412059.1_328779_329361_+	pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily	NA|242aa|up_3|NZ_AM412059.1_329290_330016_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|307aa|up_2|NZ_AM412059.1_330105_331026_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	NA|143aa|up_1|NZ_AM412059.1_331065_331494_-	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|86aa|up_0|NZ_AM412059.1_331517_331775_-	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|900aa|down_0|NZ_AM412059.1_334873_337573_-	pfam00934, PE, PE family	NA|835aa|down_1|NZ_AM412059.1_337822_340327_-	pfam00934, PE, PE family	NA|537aa|down_2|NZ_AM412059.1_340617_342228_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|303aa|down_3|NZ_AM412059.1_342251_343160_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|632aa|down_4|NZ_AM412059.1_343383_345279_+	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA	NA|539aa|down_5|NZ_AM412059.1_345275_346892_+	pfam05108, T7SS_ESX1_EccB, Type VII secretion system ESX-1, transport TM domain B	NA|1331aa|down_6|NZ_AM412059.1_346888_350881_+	TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa	NA|103aa|down_7|NZ_AM412059.1_350877_351186_+	pfam00934, PE, PE family	NA|514aa|down_8|NZ_AM412059.1_351188_352730_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|98aa|down_9|NZ_AM412059.1_352778_353072_+	TIGR03930, WXG100_ESAT6, WXG100 family type VII secretion target
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	2	333184-333294	1	PILER-CR	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,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,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA	NA|398aa|up_9|NZ_AM412059.1_321695_322889_-	COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]	NA|561aa|up_8|NZ_AM412059.1_322924_324607_+	PRK07788, PRK07788, acyl-CoA synthetase; Validated	NA|732aa|up_7|NZ_AM412059.1_324623_326819_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|378aa|up_6|NZ_AM412059.1_326932_328066_-	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|207aa|up_5|NZ_AM412059.1_328062_328683_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|194aa|up_4|NZ_AM412059.1_328779_329361_+	pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily	NA|242aa|up_3|NZ_AM412059.1_329290_330016_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|307aa|up_2|NZ_AM412059.1_330105_331026_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	NA|143aa|up_1|NZ_AM412059.1_331065_331494_-	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|86aa|up_0|NZ_AM412059.1_331517_331775_-	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|900aa|down_0|NZ_AM412059.1_334873_337573_-	pfam00934, PE, PE family	NA|835aa|down_1|NZ_AM412059.1_337822_340327_-	pfam00934, PE, PE family	NA|537aa|down_2|NZ_AM412059.1_340617_342228_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|303aa|down_3|NZ_AM412059.1_342251_343160_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|632aa|down_4|NZ_AM412059.1_343383_345279_+	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA	NA|539aa|down_5|NZ_AM412059.1_345275_346892_+	pfam05108, T7SS_ESX1_EccB, Type VII secretion system ESX-1, transport TM domain B	NA|1331aa|down_6|NZ_AM412059.1_346888_350881_+	TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa	NA|103aa|down_7|NZ_AM412059.1_350877_351186_+	pfam00934, PE, PE family	NA|514aa|down_8|NZ_AM412059.1_351188_352730_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|98aa|down_9|NZ_AM412059.1_352778_353072_+	TIGR03930, WXG100_ESAT6, WXG100 family type VII secretion target
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	3	339358-339580	2	PILER-CR	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	ATCCGCCGCTACCGCCGGTGCCGCCGGCGCCGAACAGCCCGCC	43	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	NA|732aa|up_9|NZ_AM412059.1_324623_326819_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|378aa|up_8|NZ_AM412059.1_326932_328066_-	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|207aa|up_7|NZ_AM412059.1_328062_328683_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|194aa|up_6|NZ_AM412059.1_328779_329361_+	pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily	NA|242aa|up_5|NZ_AM412059.1_329290_330016_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|307aa|up_4|NZ_AM412059.1_330105_331026_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	NA|143aa|up_3|NZ_AM412059.1_331065_331494_-	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|86aa|up_2|NZ_AM412059.1_331517_331775_-	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|917aa|up_1|NZ_AM412059.1_331859_334610_-	pfam00934, PE, PE family	NA|900aa|up_0|NZ_AM412059.1_334873_337573_-	pfam00934, PE, PE family	NA|537aa|down_0|NZ_AM412059.1_340617_342228_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|303aa|down_1|NZ_AM412059.1_342251_343160_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|632aa|down_2|NZ_AM412059.1_343383_345279_+	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA	NA|539aa|down_3|NZ_AM412059.1_345275_346892_+	pfam05108, T7SS_ESX1_EccB, Type VII secretion system ESX-1, transport TM domain B	NA|1331aa|down_4|NZ_AM412059.1_346888_350881_+	TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa	NA|103aa|down_5|NZ_AM412059.1_350877_351186_+	pfam00934, PE, PE family	NA|514aa|down_6|NZ_AM412059.1_351188_352730_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|98aa|down_7|NZ_AM412059.1_352778_353072_+	TIGR03930, WXG100_ESAT6, WXG100 family type VII secretion target	NA|97aa|down_8|NZ_AM412059.1_353101_353392_+	COG4842, COG4842, Uncharacterized protein conserved in bacteria [Function unknown]	NA|296aa|down_9|NZ_AM412059.1_353402_354290_+	pfam14011, ESX-1_EspG, EspG family
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	4	693188-693264	1	CRISPRCasFinder	no	c2c9_V-U4	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,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,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA	NA|136aa|up_9|NZ_AM412059.1_679080_679488_+	cd18696, PIN_MtVapC26-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins	NA|229aa|up_8|NZ_AM412059.1_679547_680234_-	pfam10738, Lpp-LpqN, Probable lipoprotein LpqN	NA|878aa|up_7|NZ_AM412059.1_680387_683021_+	COG3537, COG3537, Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]	NA|796aa|up_6|NZ_AM412059.1_683043_685431_-	pfam03706, LPG_synthase_TM, Lysylphosphatidylglycerol synthase TM region	NA|241aa|up_5|NZ_AM412059.1_685568_686291_+	COG2186, FadR, Transcriptional regulators [Transcription]	NA|266aa|up_4|NZ_AM412059.1_686287_687085_+	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_AM412059.1_687086_687974_+	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_AM412059.1_687979_689194_+	pfam11887, Mce4_CUP1, Cholesterol uptake porter CUP1 of Mce4, putative	NA|344aa|up_1|NZ_AM412059.1_689190_690222_+	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_AM412059.1_690218_691664_+	TIGR00996, Mtu_fam_mce, virulence factor Mce family protein	NA|517aa|down_0|NZ_AM412059.1_694399_695950_+	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_AM412059.1_696001_696394_-	cd18768, PIN_MtVapC4-C5-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins	NA|86aa|down_2|NZ_AM412059.1_696390_696648_-	COG4118, Phd, Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]	NA|412aa|down_3|NZ_AM412059.1_696830_698066_-	COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General function prediction only]	NA|138aa|down_4|NZ_AM412059.1_698316_698730_-	cd18681, PIN_MtVapC27-VapC40_like, VapC-like PIN domain of Mycobacterium tuberculosis VapC27, and VapC40, and related proteins	NA|79aa|down_5|NZ_AM412059.1_698726_698963_-	COG2002, AbrB, Regulators of stationary/sporulation gene expression [Transcription]	NA|169aa|down_6|NZ_AM412059.1_699066_699573_-	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|157aa|down_7|NZ_AM412059.1_699686_700157_-	PRK10755, PRK10755, two-component system sensor histidine kinase PmrB	NA|254aa|down_8|NZ_AM412059.1_700200_700962_-	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_AM412059.1_701018_701330_+	pfam03413, PepSY, Peptidase propeptide and YPEB domain
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	5	928678-929589	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	22	929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571|929545-929571	NZ_AM412059.1_835247-835273|NZ_AM412059.1_331974-331948|NZ_AM412059.1_334988-334962|NZ_AM412059.1_337934-337908|NZ_AM412059.1_841498-841524|NZ_AM412059.1_842776-842802|NZ_AM412059.1_928411-928437|NZ_AM412059.1_2396400-2396374|NZ_AM412059.1_335939-335913|NZ_AM412059.1_336278-336252|NZ_AM412059.1_339053-339027|NZ_AM412059.1_676287-676261|NZ_AM412059.1_838619-838645|NZ_AM412059.1_839717-839743|NZ_AM412059.1_928312-928338|NZ_AM412059.1_1216585-1216611|NZ_AM412059.1_1653758-1653732|NZ_AM412059.1_1842971-1842945|NZ_AM412059.1_2044301-2044275|NZ_AM412059.1_3765971-3765997|NZ_AM412059.1_3887303-3887329|NZ_AM412059.1_3887459-3887485	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_AM412059.1_933707_934259_-,NA|81aa|down_8|NZ_AM412059.1_939734_939977_+	NA|685aa|up_9|NZ_AM412059.1_916313_918368_-	TIGR00350, Transcriptional_regulator_LytR, cell envelope-related function transcriptional attenuator common domain	NA|390aa|up_8|NZ_AM412059.1_918533_919703_-	TIGR00737, Probable_tRNA-dihydrouridine_synthase, putative TIM-barrel protein, nifR3 family	NA|339aa|up_7|NZ_AM412059.1_919790_920807_-	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|214aa|up_6|NZ_AM412059.1_920968_921610_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|352aa|up_5|NZ_AM412059.1_921690_922746_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|131aa|up_4|NZ_AM412059.1_922797_923190_-	smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon Repressor	NA|141aa|up_3|NZ_AM412059.1_923247_923670_-	COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]	NA|97aa|up_2|NZ_AM412059.1_923631_923922_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|302aa|up_1|NZ_AM412059.1_924026_924932_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|272aa|up_0|NZ_AM412059.1_924950_925766_-	TIGR04255, hypothetical_protein, TIGR04255 family protein	NA|883aa|down_0|NZ_AM412059.1_929966_932615_-	pfam00934, PE, PE family	NA|215aa|down_1|NZ_AM412059.1_933082_933727_+	pfam14032, PknH_C, PknH-like extracellular domain	NA|184aa|down_2|NZ_AM412059.1_933707_934259_-	NA	NA|241aa|down_3|NZ_AM412059.1_934339_935062_-	COG4849, COG4849, Predicted nucleotidyltransferase [General function prediction    only]	NA|343aa|down_4|NZ_AM412059.1_935132_936161_-	COG4861, COG4861, Uncharacterized protein conserved in bacteria [Function unknown]	NA|261aa|down_5|NZ_AM412059.1_936849_937632_+	pfam01427, Peptidase_M15, D-ala-D-ala dipeptidase	NA|271aa|down_6|NZ_AM412059.1_937718_938531_+	pfam13847, Methyltransf_31, Methyltransferase domain	NA|287aa|down_7|NZ_AM412059.1_938598_939459_-	TIGR01250, Proline_iminopeptidase, proline-specific peptidase, Bacillus coagulans-type subfamily	NA|81aa|down_8|NZ_AM412059.1_939734_939977_+	NA	NA|431aa|down_9|NZ_AM412059.1_940253_941546_+	cd17329, MFS_MdtH_MDR_like, Multidrug resistance protein MdtH and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	6	930526-930655	3	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_AM412059.1_933707_934259_-,NA|81aa|down_7|NZ_AM412059.1_939734_939977_+	NA|390aa|up_9|NZ_AM412059.1_918533_919703_-	TIGR00737, Probable_tRNA-dihydrouridine_synthase, putative TIM-barrel protein, nifR3 family	NA|339aa|up_8|NZ_AM412059.1_919790_920807_-	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|214aa|up_7|NZ_AM412059.1_920968_921610_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|352aa|up_6|NZ_AM412059.1_921690_922746_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|131aa|up_5|NZ_AM412059.1_922797_923190_-	smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon Repressor	NA|141aa|up_4|NZ_AM412059.1_923247_923670_-	COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]	NA|97aa|up_3|NZ_AM412059.1_923631_923922_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|302aa|up_2|NZ_AM412059.1_924026_924932_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|272aa|up_1|NZ_AM412059.1_924950_925766_-	TIGR04255, hypothetical_protein, TIGR04255 family protein	NA|911aa|up_0|NZ_AM412059.1_927007_929740_+	pfam00934, PE, PE family	NA|215aa|down_0|NZ_AM412059.1_933082_933727_+	pfam14032, PknH_C, PknH-like extracellular domain	NA|184aa|down_1|NZ_AM412059.1_933707_934259_-	NA	NA|241aa|down_2|NZ_AM412059.1_934339_935062_-	COG4849, COG4849, Predicted nucleotidyltransferase [General function prediction    only]	NA|343aa|down_3|NZ_AM412059.1_935132_936161_-	COG4861, COG4861, Uncharacterized protein conserved in bacteria [Function unknown]	NA|261aa|down_4|NZ_AM412059.1_936849_937632_+	pfam01427, Peptidase_M15, D-ala-D-ala dipeptidase	NA|271aa|down_5|NZ_AM412059.1_937718_938531_+	pfam13847, Methyltransf_31, Methyltransferase domain	NA|287aa|down_6|NZ_AM412059.1_938598_939459_-	TIGR01250, Proline_iminopeptidase, proline-specific peptidase, Bacillus coagulans-type subfamily	NA|81aa|down_7|NZ_AM412059.1_939734_939977_+	NA	NA|431aa|down_8|NZ_AM412059.1_940253_941546_+	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_AM412059.1_941529_942534_+	COG1071, AcoA, Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	7	1214660-1215516	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	76	1215043-1215064|1215043-1215064|1215088-1215103|1215226-1215247|1215226-1215247|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361|1215343-1215361	NZ_AM412059.1_2917499-2917478|NZ_AM412059.1_2917565-2917544|NZ_AM412059.1_2071491-2071476|NZ_AM412059.1_839081-839102|NZ_AM412059.1_1220480-1220501|NZ_AM412059.1_335375-335357|NZ_AM412059.1_675951-675933|NZ_AM412059.1_841330-841348|NZ_AM412059.1_1220453-1220471|NZ_AM412059.1_1220525-1220543|NZ_AM412059.1_1628479-1628461|NZ_AM412059.1_1631305-1631287|NZ_AM412059.1_1634163-1634145|NZ_AM412059.1_1634925-1634907|NZ_AM412059.1_1974128-1974110|NZ_AM412059.1_2044475-2044457|NZ_AM412059.1_2045021-2045003|NZ_AM412059.1_2758407-2758389|NZ_AM412059.1_2761927-2761909|NZ_AM412059.1_150231-150249|NZ_AM412059.1_333366-333348|NZ_AM412059.1_336482-336464|NZ_AM412059.1_336935-336917|NZ_AM412059.1_336986-336968|NZ_AM412059.1_336995-336977|NZ_AM412059.1_339266-339248|NZ_AM412059.1_339653-339635|NZ_AM412059.1_339682-339700|NZ_AM412059.1_339776-339758|NZ_AM412059.1_364352-364334|NZ_AM412059.1_444566-444548|NZ_AM412059.1_547910-547892|NZ_AM412059.1_625142-625160|NZ_AM412059.1_625364-625382|NZ_AM412059.1_675117-675099|NZ_AM412059.1_842278-842296|NZ_AM412059.1_1093094-1093112|NZ_AM412059.1_1093742-1093760|NZ_AM412059.1_1097812-1097794|NZ_AM412059.1_1215715-1215733|NZ_AM412059.1_1216222-1216240|NZ_AM412059.1_1216474-1216492|NZ_AM412059.1_1216492-1216510|NZ_AM412059.1_1220873-1220891|NZ_AM412059.1_1488681-1488663|NZ_AM412059.1_1616425-1616407|NZ_AM412059.1_1616878-1616860|NZ_AM412059.1_1634028-1634010|NZ_AM412059.1_1634037-1634019|NZ_AM412059.1_1634250-1634232|NZ_AM412059.1_1634301-1634283|NZ_AM412059.1_1842548-1842530|NZ_AM412059.1_1843076-1843058|NZ_AM412059.1_1973402-1973384|NZ_AM412059.1_1984363-1984381|NZ_AM412059.1_2071689-2071671|NZ_AM412059.1_2279867-2279849|NZ_AM412059.1_2331122-2331104|NZ_AM412059.1_2392330-2392348|NZ_AM412059.1_2396313-2396295|NZ_AM412059.1_2538882-2538864|NZ_AM412059.1_2751723-2751705|NZ_AM412059.1_2752305-2752287|NZ_AM412059.1_3000773-3000791|NZ_AM412059.1_3000872-3000890|NZ_AM412059.1_3670073-3670091|NZ_AM412059.1_3701223-3701205|NZ_AM412059.1_3701847-3701829|NZ_AM412059.1_3702090-3702072|NZ_AM412059.1_3702222-3702204|NZ_AM412059.1_3704127-3704109|NZ_AM412059.1_3764552-3764570|NZ_AM412059.1_3764735-3764753|NZ_AM412059.1_3878152-3878170|NZ_AM412059.1_3887681-3887699|NZ_AM412059.1_3977153-3977135	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_AM412059.1_1210092_1210359_+,NA|61aa|down_3|NZ_AM412059.1_1218060_1218243_+	NA|465aa|up_9|NZ_AM412059.1_1204426_1205821_+	TIGR01137, Cystathionine_beta-synthase, cystathionine beta-synthase	NA|241aa|up_8|NZ_AM412059.1_1206022_1206745_+	pfam06271, RDD, RDD family	NA|389aa|up_7|NZ_AM412059.1_1206776_1207943_+	PRK07811, PRK07811, cystathionine gamma-synthase; Provisional	NA|165aa|up_6|NZ_AM412059.1_1208013_1208508_-	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|145aa|up_5|NZ_AM412059.1_1208693_1209128_-	pfam14155, DUF4307, Domain of unknown function (DUF4307)	NA|289aa|up_4|NZ_AM412059.1_1209229_1210096_+	TIGR03446, mycothiol_Mca, mycothiol conjugate amidase Mca	NA|89aa|up_3|NZ_AM412059.1_1210092_1210359_+	NA	NA|674aa|up_2|NZ_AM412059.1_1210345_1212367_+	COG1331, COG1331, Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]	NA|243aa|up_1|NZ_AM412059.1_1212465_1213194_-	TIGR01065, Hypothetical_UPF0073_protein_yqfA	NA|263aa|up_0|NZ_AM412059.1_1213304_1214093_+	PRK14828, PRK14828, undecaprenyl pyrophosphate synthase; Provisional	NA|107aa|down_0|NZ_AM412059.1_1216875_1217196_+	COG0020, UppS, Undecaprenyl pyrophosphate synthase [Lipid metabolism]	NA|145aa|down_1|NZ_AM412059.1_1217348_1217783_+	pfam00934, PE, PE family	NA|55aa|down_2|NZ_AM412059.1_1217884_1218049_+	smart00637, CBD_II, CBD_II domain	NA|61aa|down_3|NZ_AM412059.1_1218060_1218243_+	NA	NA|152aa|down_4|NZ_AM412059.1_1218434_1218890_+	pfam01670, Glyco_hydro_12, Glycosyl hydrolase family 12	NA|851aa|down_5|NZ_AM412059.1_1219304_1221857_+	pfam00934, PE, PE family	NA|313aa|down_6|NZ_AM412059.1_1222074_1223013_-	PRK05439, PRK05439, pantothenate kinase; Provisional	NA|427aa|down_7|NZ_AM412059.1_1223400_1224681_+	PRK00011, glyA, serine hydroxymethyltransferase; Reviewed	NA|276aa|down_8|NZ_AM412059.1_1224785_1225613_+	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|434aa|down_9|NZ_AM412059.1_1225823_1227125_+	COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family domains [General    function prediction only]
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	8	2071161-2071415	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	2071242-2071259|2071242-2071259|2071332-2071349	NZ_AM412059.1_402332-402315|NZ_AM412059.1_608504-608487|NZ_AM412059.1_3396148-3396131	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_AM412059.1_2070520_2070784_-,NA	NA|165aa|up_9|NZ_AM412059.1_2056870_2057365_+	pfam02577, DNase-RNase, Bifunctional nuclease	NA|226aa|up_8|NZ_AM412059.1_2057712_2058390_+	cd01105, HTH_GlnR-like, Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators	NA|942aa|up_7|NZ_AM412059.1_2058748_2061574_+	PRK05367, PRK05367, aminomethyl-transferring glycine dehydrogenase	NA|287aa|up_6|NZ_AM412059.1_2061800_2062661_-	PRK03204, PRK03204, haloalkane dehalogenase; Provisional	NA|289aa|up_5|NZ_AM412059.1_2062701_2063568_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|629aa|up_4|NZ_AM412059.1_2063572_2065459_-	TIGR00976, Hypothetical_protein_Rv1835c/MT1883/Mb1866c	NA|678aa|up_3|NZ_AM412059.1_2065474_2067508_-	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_AM412059.1_2067627_2069853_-	PRK02999, PRK02999, malate synthase G; Provisional	NA|132aa|up_1|NZ_AM412059.1_2070128_2070524_-	COG1848, COG1848, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]	NA|88aa|up_0|NZ_AM412059.1_2070520_2070784_-	NA	NA|350aa|down_0|NZ_AM412059.1_2072551_2073601_-	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]	NA|456aa|down_1|NZ_AM412059.1_2073600_2074968_-	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]	NA|480aa|down_2|NZ_AM412059.1_2075141_2076581_-	PRK07807, PRK07807, GuaB1 family IMP dehydrogenase-related protein	NA|317aa|down_3|NZ_AM412059.1_2078093_2079044_-	cd07326, M56_BlaR1_MecR1_like, Peptidase M56-like including those in BlaR1 and MecR1, integral membrane metallopeptidase	NA|139aa|down_4|NZ_AM412059.1_2079058_2079475_-	COG3682, COG3682, Predicted transcriptional regulator [Transcription]	NA|141aa|down_5|NZ_AM412059.1_2079752_2080175_+	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_AM412059.1_2080223_2080526_+	pfam00547, Urease_gamma, Urease, gamma subunit	NA|105aa|down_7|NZ_AM412059.1_2080522_2080837_+	PRK13202, ureB, urease subunit beta; Reviewed	NA|578aa|down_8|NZ_AM412059.1_2080836_2082570_+	PRK13206, ureC, urease subunit alpha; Reviewed	NA|212aa|down_9|NZ_AM412059.1_2082569_2083205_+	COG0830, UreF, Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	9	2152892-2153017	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_AM412059.1_2142867_2143275_-,NA|127aa|down_5|NZ_AM412059.1_2160626_2161007_-	NA|216aa|up_9|NZ_AM412059.1_2136181_2136829_-	pfam14081, DUF4262, Domain of unknown function (DUF4262)	NA|741aa|up_8|NZ_AM412059.1_2136835_2139058_-	PRK15061, PRK15061, catalase/peroxidase	NA|148aa|up_7|NZ_AM412059.1_2139095_2139539_-	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]	NA|198aa|up_6|NZ_AM412059.1_2139652_2140246_-	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|202aa|up_5|NZ_AM412059.1_2140328_2140934_-	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|335aa|up_4|NZ_AM412059.1_2141033_2142038_-	cd08275, MDR3, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family	NA|251aa|up_3|NZ_AM412059.1_2142137_2142890_+	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_AM412059.1_2142867_2143275_-	NA	NA|767aa|up_1|NZ_AM412059.1_2143409_2145710_+	PLN02892, PLN02892, isocitrate lyase	NA|1836aa|up_0|NZ_AM412059.1_2145879_2151387_-	pfam00823, PPE, PPE family	NA|155aa|down_0|NZ_AM412059.1_2155137_2155602_-	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_AM412059.1_2155699_2156563_+	cd07987, LPLAT_MGAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: MGAT-like	NA|424aa|down_2|NZ_AM412059.1_2156600_2157872_-	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|372aa|down_3|NZ_AM412059.1_2158143_2159259_+	COG1680, AmpC, Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]	NA|447aa|down_4|NZ_AM412059.1_2159249_2160590_+	pfam00144, Beta-lactamase, Beta-lactamase	NA|127aa|down_5|NZ_AM412059.1_2160626_2161007_-	NA	NA|621aa|down_6|NZ_AM412059.1_2161163_2163026_+	PRK12476, PRK12476, putative fatty-acid--CoA ligase; Provisional	NA|160aa|down_7|NZ_AM412059.1_2163033_2163513_-	pfam09167, DUF1942, Domain of unknown function (DUF1942)	NA|258aa|down_8|NZ_AM412059.1_2163749_2164523_+	COG3361, COG3361, Uncharacterized conserved protein [Function unknown]	NA|256aa|down_9|NZ_AM412059.1_2164526_2165294_-	PRK05867, PRK05867, SDR family oxidoreductase
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	10	3065128-3066555	4,4,4,5	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-D,Type III-C	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	13,18,19,13	19	TypeIII-A,TypeIII-B,TypeIII-D,TypeIII-C	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|85aa|up_8|NZ_AM412059.1_3058407_3058662_-,NA|135aa|up_7|NZ_AM412059.1_3058809_3059214_+,NA|64aa|up_6|NZ_AM412059.1_3059210_3059402_+,NA|86aa|up_4|NZ_AM412059.1_3060988_3061246_+,NA|104aa|up_3|NZ_AM412059.1_3061350_3061662_+,NA|203aa|up_2|NZ_AM412059.1_3062081_3062690_+,NA	NA|92aa|up_9|NZ_AM412059.1_3057956_3058232_+	COG4453, COG4453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|85aa|up_8|NZ_AM412059.1_3058407_3058662_-	NA	NA|135aa|up_7|NZ_AM412059.1_3058809_3059214_+	NA	NA|64aa|up_6|NZ_AM412059.1_3059210_3059402_+	NA	NA|385aa|up_5|NZ_AM412059.1_3059600_3060755_+	pfam00665, rve, Integrase core domain	NA|86aa|up_4|NZ_AM412059.1_3060988_3061246_+	NA	NA|104aa|up_3|NZ_AM412059.1_3061350_3061662_+	NA	NA|203aa|up_2|NZ_AM412059.1_3062081_3062690_+	NA	NA|470aa|up_1|NZ_AM412059.1_3062760_3064170_+	pfam00665, rve, Integrase core domain	NA|271aa|up_0|NZ_AM412059.1_3064166_3064979_+	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	NA|421aa|down_0|NZ_AM412059.1_3066581_3067843_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas2|114aa|down_1|NZ_AM412059.1_3070096_3070438_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|339aa|down_2|NZ_AM412059.1_3070438_3071455_-	TIGR00287, CRISPR-associated_endonuclease_Cas1, CRISPR-associated endonuclease Cas1	csm5gr7|376aa|down_3|NZ_AM412059.1_3072711_3073839_-	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm4gr5|303aa|down_4|NZ_AM412059.1_3073835_3074744_-	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm3gr7|237aa|down_5|NZ_AM412059.1_3074724_3075435_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|125aa|down_6|NZ_AM412059.1_3075444_3075819_-	TIGR01870, CRISPR_type_III-associated_protein_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2	cas10|813aa|down_7|NZ_AM412059.1_3075815_3078254_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|241aa|down_8|NZ_AM412059.1_3078250_3078973_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	NA|182aa|down_9|NZ_AM412059.1_3079372_3079918_-	COG4293, COG4293, Uncharacterized protein conserved in bacteria [Function unknown]
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	11	3067878-3070048	5,5,6	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-D,Type III-C	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-D,TypeIII-C	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|85aa|up_9|NZ_AM412059.1_3058407_3058662_-,NA|135aa|up_8|NZ_AM412059.1_3058809_3059214_+,NA|64aa|up_7|NZ_AM412059.1_3059210_3059402_+,NA|86aa|up_5|NZ_AM412059.1_3060988_3061246_+,NA|104aa|up_4|NZ_AM412059.1_3061350_3061662_+,NA|203aa|up_3|NZ_AM412059.1_3062081_3062690_+,NA	NA|85aa|up_9|NZ_AM412059.1_3058407_3058662_-	NA	NA|135aa|up_8|NZ_AM412059.1_3058809_3059214_+	NA	NA|64aa|up_7|NZ_AM412059.1_3059210_3059402_+	NA	NA|385aa|up_6|NZ_AM412059.1_3059600_3060755_+	pfam00665, rve, Integrase core domain	NA|86aa|up_5|NZ_AM412059.1_3060988_3061246_+	NA	NA|104aa|up_4|NZ_AM412059.1_3061350_3061662_+	NA	NA|203aa|up_3|NZ_AM412059.1_3062081_3062690_+	NA	NA|470aa|up_2|NZ_AM412059.1_3062760_3064170_+	pfam00665, rve, Integrase core domain	NA|271aa|up_1|NZ_AM412059.1_3064166_3064979_+	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	NA|421aa|up_0|NZ_AM412059.1_3066581_3067843_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas2|114aa|down_0|NZ_AM412059.1_3070096_3070438_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|339aa|down_1|NZ_AM412059.1_3070438_3071455_-	TIGR00287, CRISPR-associated_endonuclease_Cas1, CRISPR-associated endonuclease Cas1	csm5gr7|376aa|down_2|NZ_AM412059.1_3072711_3073839_-	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm4gr5|303aa|down_3|NZ_AM412059.1_3073835_3074744_-	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm3gr7|237aa|down_4|NZ_AM412059.1_3074724_3075435_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|125aa|down_5|NZ_AM412059.1_3075444_3075819_-	TIGR01870, CRISPR_type_III-associated_protein_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2	cas10|813aa|down_6|NZ_AM412059.1_3075815_3078254_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|241aa|down_7|NZ_AM412059.1_3078250_3078973_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	NA|182aa|down_8|NZ_AM412059.1_3079372_3079918_-	COG4293, COG4293, Uncharacterized protein conserved in bacteria [Function unknown]	NA|295aa|down_9|NZ_AM412059.1_3080189_3081074_-	COG2253, COG2253, Uncharacterized conserved protein [Function unknown]
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	12	4033658-4033983	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	4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704|4033683-4033704	NZ_AM412059.1_971884-971863|NZ_AM412059.1_1842649-1842628|NZ_AM412059.1_2396771-2396750|NZ_AM412059.1_3701222-3701201|NZ_AM412059.1_3892841-3892862|NZ_AM412059.1_335188-335167|NZ_AM412059.1_335374-335353|NZ_AM412059.1_336481-336460|NZ_AM412059.1_336985-336964|NZ_AM412059.1_339079-339058|NZ_AM412059.1_673667-673646|NZ_AM412059.1_675116-675095|NZ_AM412059.1_841178-841199|NZ_AM412059.1_930464-930443|NZ_AM412059.1_971404-971383|NZ_AM412059.1_1093095-1093116|NZ_AM412059.1_1191829-1191808|NZ_AM412059.1_1194354-1194333|NZ_AM412059.1_1488029-1488008|NZ_AM412059.1_1488680-1488659|NZ_AM412059.1_1634924-1634903|NZ_AM412059.1_1973548-1973527|NZ_AM412059.1_1974778-1974757|NZ_AM412059.1_1985153-1985174|NZ_AM412059.1_2044828-2044807|NZ_AM412059.1_2760902-2760881|NZ_AM412059.1_3109256-3109277|NZ_AM412059.1_3704126-3704105|NZ_AM412059.1_3742651-3742672|NZ_AM412059.1_3881749-3881770|NZ_AM412059.1_3882073-3882094|NZ_AM412059.1_3882697-3882718|NZ_AM412059.1_3887748-3887769|NZ_AM412059.1_3889842-3889863|NZ_AM412059.1_3977053-3977032|NZ_AM412059.1_3977152-3977131	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_AM412059.1_4027160_4027739_-,NA|52aa|up_1|NZ_AM412059.1_4032571_4032727_-,NA|100aa|down_1|NZ_AM412059.1_4034642_4034942_-,NA|257aa|down_8|NZ_AM412059.1_4040907_4041678_-	NA|402aa|up_9|NZ_AM412059.1_4021066_4022272_-	PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated	NA|550aa|up_8|NZ_AM412059.1_4022357_4024007_+	cd07302, CHD, cyclase homology domain	NA|935aa|up_7|NZ_AM412059.1_4024003_4026808_-	PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated	NA|193aa|up_6|NZ_AM412059.1_4027160_4027739_-	NA	NA|68aa|up_5|NZ_AM412059.1_4027878_4028082_-	COG1278, CspC, Cold shock proteins [Transcription]	cas3|772aa|up_4|NZ_AM412059.1_4028331_4030647_+	TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase	NA|95aa|up_3|NZ_AM412059.1_4030783_4031068_+	pfam00934, PE, PE family	NA|346aa|up_2|NZ_AM412059.1_4031391_4032429_+	pfam18621, DUF5628, Family of unknown function (DUF5628)	NA|52aa|up_1|NZ_AM412059.1_4032571_4032727_-	NA	NA|105aa|up_0|NZ_AM412059.1_4033182_4033497_+	pfam00934, PE, PE family	NA|126aa|down_0|NZ_AM412059.1_4034302_4034680_-	TIGR03816, tadE_like_DECH, helicase/secretion neighborhood TadE-like protein	NA|100aa|down_1|NZ_AM412059.1_4034642_4034942_-	NA	NA|69aa|down_2|NZ_AM412059.1_4034965_4035172_-	pfam14029, DUF4244, Protein of unknown function (DUF4244)	NA|192aa|down_3|NZ_AM412059.1_4035181_4035757_-	COG2064, TadC, Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]	NA|267aa|down_4|NZ_AM412059.1_4035780_4036581_-	COG4965, TadB, Flp pilus assembly protein TadB [Intracellular trafficking and secretion]	NA|388aa|down_5|NZ_AM412059.1_4036577_4037741_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|351aa|down_6|NZ_AM412059.1_4037737_4038790_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|288aa|down_7|NZ_AM412059.1_4039289_4040153_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|257aa|down_8|NZ_AM412059.1_4040907_4041678_-	NA	NA|549aa|down_9|NZ_AM412059.1_4041674_4043321_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	13	4034060-4034138	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_AM412059.1_4027160_4027739_-,NA|52aa|up_1|NZ_AM412059.1_4032571_4032727_-,NA|100aa|down_1|NZ_AM412059.1_4034642_4034942_-,NA|257aa|down_8|NZ_AM412059.1_4040907_4041678_-	NA|402aa|up_9|NZ_AM412059.1_4021066_4022272_-	PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated	NA|550aa|up_8|NZ_AM412059.1_4022357_4024007_+	cd07302, CHD, cyclase homology domain	NA|935aa|up_7|NZ_AM412059.1_4024003_4026808_-	PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated	NA|193aa|up_6|NZ_AM412059.1_4027160_4027739_-	NA	NA|68aa|up_5|NZ_AM412059.1_4027878_4028082_-	COG1278, CspC, Cold shock proteins [Transcription]	cas3|772aa|up_4|NZ_AM412059.1_4028331_4030647_+	TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase	NA|95aa|up_3|NZ_AM412059.1_4030783_4031068_+	pfam00934, PE, PE family	NA|346aa|up_2|NZ_AM412059.1_4031391_4032429_+	pfam18621, DUF5628, Family of unknown function (DUF5628)	NA|52aa|up_1|NZ_AM412059.1_4032571_4032727_-	NA	NA|105aa|up_0|NZ_AM412059.1_4033182_4033497_+	pfam00934, PE, PE family	NA|126aa|down_0|NZ_AM412059.1_4034302_4034680_-	TIGR03816, tadE_like_DECH, helicase/secretion neighborhood TadE-like protein	NA|100aa|down_1|NZ_AM412059.1_4034642_4034942_-	NA	NA|69aa|down_2|NZ_AM412059.1_4034965_4035172_-	pfam14029, DUF4244, Protein of unknown function (DUF4244)	NA|192aa|down_3|NZ_AM412059.1_4035181_4035757_-	COG2064, TadC, Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]	NA|267aa|down_4|NZ_AM412059.1_4035780_4036581_-	COG4965, TadB, Flp pilus assembly protein TadB [Intracellular trafficking and secretion]	NA|388aa|down_5|NZ_AM412059.1_4036577_4037741_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|351aa|down_6|NZ_AM412059.1_4037737_4038790_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|288aa|down_7|NZ_AM412059.1_4039289_4040153_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|257aa|down_8|NZ_AM412059.1_4040907_4041678_-	NA	NA|549aa|down_9|NZ_AM412059.1_4041674_4043321_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]
GCF_000967285.1_ASM96728v1	NZ_AM412059	Mycobacterium tuberculosis variant bovis BCG str. Moreau RDJ isolate SL21 FAP RJ Passage B8S2 vaccine culture	14	4050321-4050409	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_6|NZ_AM412059.1_4040907_4041678_-,NA|233aa|up_0|NZ_AM412059.1_4049425_4050124_-,NA|126aa|down_6|NZ_AM412059.1_4055644_4056022_+	NA|388aa|up_9|NZ_AM412059.1_4036577_4037741_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|351aa|up_8|NZ_AM412059.1_4037737_4038790_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|288aa|up_7|NZ_AM412059.1_4039289_4040153_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|257aa|up_6|NZ_AM412059.1_4040907_4041678_-	NA	NA|549aa|up_5|NZ_AM412059.1_4041674_4043321_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]	NA|288aa|up_4|NZ_AM412059.1_4043317_4044181_-	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_AM412059.1_4044173_4045100_-	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_AM412059.1_4045101_4046727_-	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_AM412059.1_4047434_4049390_+	PRK00174, PRK00174, acetyl-CoA synthetase; Provisional	NA|233aa|up_0|NZ_AM412059.1_4049425_4050124_-	NA	NA|173aa|down_0|NZ_AM412059.1_4050469_4050988_+	pfam07332, Phage_holin_3_6, Putative Actinobacterial Holin-X, holin superfamily III	NA|328aa|down_1|NZ_AM412059.1_4050988_4051972_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|398aa|down_2|NZ_AM412059.1_4051964_4053158_-	pfam13365, Trypsin_2, Trypsin-like peptidase domain	NA|274aa|down_3|NZ_AM412059.1_4053163_4053985_-	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_AM412059.1_4054116_4054800_-	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins	NA|246aa|down_5|NZ_AM412059.1_4054799_4055537_-	COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]	NA|126aa|down_6|NZ_AM412059.1_4055644_4056022_+	NA	NA|225aa|down_7|NZ_AM412059.1_4056120_4056795_+	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]	NA|265aa|down_8|NZ_AM412059.1_4056900_4057695_-	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_AM412059.1_4057701_4058157_-	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
