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_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	1	329228-329338	1	PILER-CR	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Orphan	CCGCCGTTGCCGCCGTTGCCGATCA	25	0	0	NA	NA	NA	2	2	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA|61aa|up_0|NC_015758.1_327561_327744_-,NA	NA|398aa|up_9|NC_015758.1_317739_318933_-	COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]	NA|561aa|up_8|NC_015758.1_318968_320651_+	PRK07788, PRK07788, acyl-CoA synthetase; Validated	NA|732aa|up_7|NC_015758.1_320667_322863_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|378aa|up_6|NC_015758.1_322976_324110_-	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|207aa|up_5|NC_015758.1_324106_324727_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|194aa|up_4|NC_015758.1_324823_325405_+	pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily	NA|242aa|up_3|NC_015758.1_325334_326060_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|307aa|up_2|NC_015758.1_326149_327070_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	NA|143aa|up_1|NC_015758.1_327109_327538_-	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|61aa|up_0|NC_015758.1_327561_327744_-	NA	NA|838aa|down_0|NC_015758.1_333278_335792_-	pfam00934, PE, PE family	NA|537aa|down_1|NC_015758.1_336083_337694_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|303aa|down_2|NC_015758.1_337717_338626_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|632aa|down_3|NC_015758.1_338849_340745_+	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA	NA|539aa|down_4|NC_015758.1_340741_342358_+	pfam05108, T7SS_ESX1_EccB, Type VII secretion system ESX-1, transport TM domain B	NA|1331aa|down_5|NC_015758.1_342354_346347_+	TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa	NA|103aa|down_6|NC_015758.1_346343_346652_+	pfam00934, PE, PE family	NA|514aa|down_7|NC_015758.1_346654_348196_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|98aa|down_8|NC_015758.1_348244_348538_+	TIGR03930, WXG100_ESAT6, WXG100 family type VII secretion target	NA|97aa|down_9|NC_015758.1_348567_348858_+	COG4842, COG4842, Uncharacterized protein conserved in bacteria [Function unknown]
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	2	363228-363926	1	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Orphan	TTCGCGAAGCCGATGTTGTAGCTGCCGGTGTTG	33	2	2	363516-363557|363591-363623	NC_015758.1_371531-371572|NC_015758.1_370346-370378	NA	10	10	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA|101aa|up_4|NC_015758.1_360240_360543_+,NA|161aa|down_1|NC_015758.1_373320_373803_-,NA|410aa|down_5|NC_015758.1_375919_377149_+	NA|262aa|up_9|NC_015758.1_354890_355676_+	PRK14103, PRK14103, trans-aconitate 2-methyltransferase; Provisional	NA|268aa|up_8|NC_015758.1_355664_356468_-	COG4424, COG4424, Uncharacterized protein conserved in bacteria [Function unknown]	NA|466aa|up_7|NC_015758.1_356477_357875_-	cd16027, SGSH, N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase)	NA|607aa|up_6|NC_015758.1_358053_359874_+	pfam00934, PE, PE family	NA|76aa|up_5|NC_015758.1_360016_360244_+	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|101aa|up_4|NC_015758.1_360240_360543_+	NA	NA|74aa|up_3|NC_015758.1_360590_360812_+	PHA01748, PHA01748, hypothetical protein	NA|142aa|up_2|NC_015758.1_360808_361234_+	cd18755, PIN_MtVapC3_VapC21-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC3, VapC21 and related proteins	NA|211aa|up_1|NC_015758.1_361369_362002_+	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|303aa|up_0|NC_015758.1_361998_362907_+	cd09810, LPOR_like_SDR_c_like, light-dependent protochlorophyllide reductase (LPOR)-like, classical (c)-like SDRs	NA|224aa|down_0|NC_015758.1_372661_373333_+	TIGR02476, BluB, 5,6-dimethylbenzimidazole synthase	NA|161aa|down_1|NC_015758.1_373320_373803_-	NA	NA|239aa|down_2|NC_015758.1_373860_374577_+	cd03392, PAP2_like_2, PAP2_like_2 proteins	NA|219aa|down_3|NC_015758.1_374678_375335_+	COG3786, COG3786, Uncharacterized protein conserved in bacteria [Function unknown]	NA|164aa|down_4|NC_015758.1_375404_375896_-	pfam13577, SnoaL_4, SnoaL-like domain	NA|410aa|down_5|NC_015758.1_375919_377149_+	NA	NA|621aa|down_6|NC_015758.1_377303_379166_+	COG0443, DnaK, Molecular chaperone [Posttranslational modification, protein turnover, chaperones]	NA|129aa|down_7|NC_015758.1_379237_379624_+	COG0326, HtpG, Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]	NA|212aa|down_8|NC_015758.1_379626_380262_-	pfam11259, DUF3060, Protein of unknown function (DUF3060)	NA|295aa|down_9|NC_015758.1_380349_381234_+	COG2273, SKN1, Beta-glucanase/Beta-glucan synthetase [Carbohydrate transport and metabolism]
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	3	688888-688964	2	CRISPRCasFinder	no	c2c9_V-U4	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,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,csm3gr7,csm2gr11,cas10,cas6	NA,NA|57aa|down_9|NC_015758.1_696857_697028_+	NA|72aa|up_9|NC_015758.1_674572_674788_+	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|136aa|up_8|NC_015758.1_674784_675192_+	cd18696, PIN_MtVapC26-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins	NA|229aa|up_7|NC_015758.1_675251_675938_-	pfam10738, Lpp-LpqN, Probable lipoprotein LpqN	NA|878aa|up_6|NC_015758.1_676091_678725_+	COG3537, COG3537, Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]	NA|241aa|up_5|NC_015758.1_681271_681994_+	COG2186, FadR, Transcriptional regulators [Transcription]	NA|266aa|up_4|NC_015758.1_681990_682788_+	COG0767, Ttg2B, ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|296aa|up_3|NC_015758.1_682789_683677_+	COG0767, Ttg2B, ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|405aa|up_2|NC_015758.1_683682_684897_+	pfam11887, Mce4_CUP1, Cholesterol uptake porter CUP1 of Mce4, putative	NA|344aa|up_1|NC_015758.1_684893_685925_+	COG1463, Ttg2C, ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|482aa|up_0|NC_015758.1_685921_687367_+	TIGR00996, Mtu_fam_mce, virulence factor Mce family protein	NA|517aa|down_0|NC_015758.1_690099_691650_+	COG1463, Ttg2C, ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|131aa|down_1|NC_015758.1_691701_692094_-	cd18768, PIN_MtVapC4-C5-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins	NA|86aa|down_2|NC_015758.1_692090_692348_-	COG4118, Phd, Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]	NA|412aa|down_3|NC_015758.1_692530_693766_-	COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General function prediction only]	NA|138aa|down_4|NC_015758.1_694016_694430_-	cd18681, PIN_MtVapC27-VapC40_like, VapC-like PIN domain of Mycobacterium tuberculosis VapC27, and VapC40, and related proteins	NA|79aa|down_5|NC_015758.1_694426_694663_-	COG2002, AbrB, Regulators of stationary/sporulation gene expression [Transcription]	NA|169aa|down_6|NC_015758.1_694766_695273_-	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|157aa|down_7|NC_015758.1_695386_695857_-	PRK10755, PRK10755, two-component system sensor histidine kinase PmrB	NA|254aa|down_8|NC_015758.1_695900_696662_-	COG0745, OmpR, Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]	NA|57aa|down_9|NC_015758.1_696857_697028_+	NA
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	4	836377-837005	1	CRT	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Orphan	NACGGCGGGGCCGGCGGGGCCGGCGG	26	1	4	836634-836652|836634-836652|836634-836652|836634-836652	NC_015758.1_2849141-2849123|NC_015758.1_883458-883440|NC_015758.1_980987-981005|NC_015758.1_1571907-1571889	NA	10	10	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA|71aa|up_9|NC_015758.1_827087_827300_+,NA|176aa|up_6|NC_015758.1_829164_829692_+,NA|186aa|up_4|NC_015758.1_831274_831832_-,NA|46aa|down_2|NC_015758.1_839152_839290_-,NA|82aa|down_3|NC_015758.1_839448_839694_+,NA|242aa|down_9|NC_015758.1_848153_848879_-	NA|71aa|up_9|NC_015758.1_827087_827300_+	NA	NA|183aa|up_8|NC_015758.1_827448_827997_+	TIGR03086, TIGR03086, TIGR03086 family protein	NA|283aa|up_7|NC_015758.1_828201_829050_+	pfam10774, DUF4226, Domain of unknown function (DUF4226)	NA|176aa|up_6|NC_015758.1_829164_829692_+	NA	NA|176aa|up_5|NC_015758.1_830369_830897_+	pfam00934, PE, PE family	NA|186aa|up_4|NC_015758.1_831274_831832_-	NA	NA|169aa|up_3|NC_015758.1_831828_832335_-	pfam12728, HTH_17, Helix-turn-helix domain	NA|49aa|up_2|NC_015758.1_832447_832594_-	TIGR01692, 3-hydroxyisobutyrate_dehydrogenase_mitochondrial, 3-hydroxyisobutyrate dehydrogenase	NA|176aa|up_1|NC_015758.1_832542_833070_+	TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase	NA|844aa|up_0|NC_015758.1_833089_835621_+	pfam00934, PE, PE family	NA|86aa|down_0|NC_015758.1_838362_838620_+	pfam01402, RHH_1, Ribbon-helix-helix protein, copG family	NA|143aa|down_1|NC_015758.1_838643_839072_+	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|46aa|down_2|NC_015758.1_839152_839290_-	NA	NA|82aa|down_3|NC_015758.1_839448_839694_+	NA	NA|295aa|down_4|NC_015758.1_839762_840647_-	TIGR01692, 3-hydroxyisobutyrate_dehydrogenase_mitochondrial, 3-hydroxyisobutyrate dehydrogenase	NA|391aa|down_5|NC_015758.1_840657_841830_-	cd01162, IBD, Isobutyryl-CoA dehydrogenase	NA|511aa|down_6|NC_015758.1_841836_843369_-	cd07085, ALDH_F6_MMSDH, Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2	NA|584aa|down_7|NC_015758.1_843574_845326_+	pfam00934, PE, PE family	NA|646aa|down_8|NC_015758.1_845515_847453_-	pfam00823, PPE, PPE family	NA|242aa|down_9|NC_015758.1_848153_848879_-	NA
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	5	922676-923587	2	CRT	no	csa3	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Type I-A	CGGGGCCGGCGGGGCCGGCGG	21	1	20	923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569|923543-923569	NC_015758.1_830893-830919|NC_015758.1_838131-838157|NC_015758.1_922409-922435|NC_015758.1_328018-327992|NC_015758.1_331040-331014|NC_015758.1_333390-333364|NC_015758.1_2413150-2413124|NC_015758.1_834355-834381|NC_015758.1_835501-835527|NC_015758.1_922310-922336|NC_015758.1_1211243-1211269|NC_015758.1_3787007-3787033|NC_015758.1_3923968-3923994|NC_015758.1_3924124-3924150|NC_015758.1_331991-331965|NC_015758.1_332330-332304|NC_015758.1_671991-671965|NC_015758.1_1659344-1659318|NC_015758.1_1861400-1861374|NC_015758.1_2060691-2060665	NA	19	19	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA,NA|184aa|down_2|NC_015758.1_927696_928248_-,NA|81aa|down_8|NC_015758.1_933729_933972_+	NA|685aa|up_9|NC_015758.1_910311_912366_-	TIGR00350, Transcriptional_regulator_LytR, cell envelope-related function transcriptional attenuator common domain	NA|390aa|up_8|NC_015758.1_912531_913701_-	TIGR00737, Probable_tRNA-dihydrouridine_synthase, putative TIM-barrel protein, nifR3 family	NA|339aa|up_7|NC_015758.1_913788_914805_-	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|214aa|up_6|NC_015758.1_914966_915608_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|352aa|up_5|NC_015758.1_915688_916744_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|131aa|up_4|NC_015758.1_916795_917188_-	smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon Repressor	NA|141aa|up_3|NC_015758.1_917245_917668_-	COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]	NA|97aa|up_2|NC_015758.1_917629_917920_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|302aa|up_1|NC_015758.1_918024_918930_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|272aa|up_0|NC_015758.1_918948_919764_-	TIGR04255, hypothetical_protein, TIGR04255 family protein	NA|883aa|down_0|NC_015758.1_923955_926604_-	pfam00934, PE, PE family	NA|215aa|down_1|NC_015758.1_927071_927716_+	pfam14032, PknH_C, PknH-like extracellular domain	NA|184aa|down_2|NC_015758.1_927696_928248_-	NA	NA|241aa|down_3|NC_015758.1_928328_929051_-	COG4849, COG4849, Predicted nucleotidyltransferase [General function prediction    only]	NA|343aa|down_4|NC_015758.1_929121_930150_-	COG4861, COG4861, Uncharacterized protein conserved in bacteria [Function unknown]	NA|263aa|down_5|NC_015758.1_930838_931627_+	pfam01427, Peptidase_M15, D-ala-D-ala dipeptidase	NA|271aa|down_6|NC_015758.1_931713_932526_+	pfam13847, Methyltransf_31, Methyltransferase domain	NA|287aa|down_7|NC_015758.1_932593_933454_-	TIGR01250, Proline_iminopeptidase, proline-specific peptidase, Bacillus coagulans-type subfamily	NA|81aa|down_8|NC_015758.1_933729_933972_+	NA	NA|431aa|down_9|NC_015758.1_934248_935541_+	cd17329, MFS_MdtH_MDR_like, Multidrug resistance protein MdtH and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	6	1209270-1210126	3	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Orphan	GGCGGTGTCGGCGGTGCCGGCGG	23	4	79	1209653-1209674|1209698-1209713|1209836-1209857|1209836-1209857|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971|1209953-1209971	NC_015758.1_2948004-2947983|NC_015758.1_2087938-2087923|NC_015758.1_834865-834886|NC_015758.1_1215138-1215159|NC_015758.1_1576108-1576090|NC_015758.1_833935-833953|NC_015758.1_1210922-1210940|NC_015758.1_1215111-1215129|NC_015758.1_1215183-1215201|NC_015758.1_331427-331409|NC_015758.1_671655-671637|NC_015758.1_1633953-1633935|NC_015758.1_1636752-1636734|NC_015758.1_1639607-1639589|NC_015758.1_1640369-1640351|NC_015758.1_1989327-1989309|NC_015758.1_2060865-2060847|NC_015758.1_2061411-2061393|NC_015758.1_2327783-2327765|NC_015758.1_2788894-2788876|NC_015758.1_2792422-2792404|NC_015758.1_335147-335165|NC_015758.1_620845-620863|NC_015758.1_621067-621085|NC_015758.1_837633-837651|NC_015758.1_1087339-1087357|NC_015758.1_1087987-1088005|NC_015758.1_1210325-1210343|NC_015758.1_1210841-1210859|NC_015758.1_1211132-1211150|NC_015758.1_1211150-1211168|NC_015758.1_1215429-1215447|NC_015758.1_2000732-2000750|NC_015758.1_2408972-2408990|NC_015758.1_2681569-2681587|NC_015758.1_3031162-3031180|NC_015758.1_3031261-3031279|NC_015758.1_3686055-3686073|NC_015758.1_3785579-3785597|NC_015758.1_3785762-3785780|NC_015758.1_3785930-3785948|NC_015758.1_3915170-3915188|NC_015758.1_3924346-3924364|NC_015758.1_4070281-4070299|NC_015758.1_4070290-4070308|NC_015758.1_328183-328165|NC_015758.1_329409-329391|NC_015758.1_332534-332516|NC_015758.1_334722-334704|NC_015758.1_334851-334833|NC_015758.1_335118-335100|NC_015758.1_335241-335223|NC_015758.1_359818-359800|NC_015758.1_440163-440145|NC_015758.1_543491-543473|NC_015758.1_670821-670803|NC_015758.1_1092057-1092039|NC_015758.1_1493850-1493832|NC_015758.1_1622370-1622352|NC_015758.1_1639472-1639454|NC_015758.1_1639481-1639463|NC_015758.1_1639694-1639676|NC_015758.1_1639745-1639727|NC_015758.1_1860977-1860959|NC_015758.1_1861505-1861487|NC_015758.1_1988601-1988583|NC_015758.1_2088136-2088118|NC_015758.1_2296319-2296301|NC_015758.1_2347619-2347601|NC_015758.1_2413063-2413045|NC_015758.1_2555719-2555701|NC_015758.1_2782218-2782200|NC_015758.1_2782800-2782782|NC_015758.1_3722118-3722100|NC_015758.1_3722742-3722724|NC_015758.1_3722985-3722967|NC_015758.1_3723117-3723099|NC_015758.1_3725142-3725124|NC_015758.1_4013526-4013508	NA	16	16	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA|89aa|up_3|NC_015758.1_1204702_1204969_+,NA|61aa|down_3|NC_015758.1_1212718_1212901_+	NA|465aa|up_9|NC_015758.1_1199036_1200431_+	TIGR01137, Cystathionine_beta-synthase, cystathionine beta-synthase	NA|241aa|up_8|NC_015758.1_1200632_1201355_+	pfam06271, RDD, RDD family	NA|389aa|up_7|NC_015758.1_1201386_1202553_+	PRK07811, PRK07811, cystathionine gamma-synthase; Provisional	NA|165aa|up_6|NC_015758.1_1202623_1203118_-	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|145aa|up_5|NC_015758.1_1203303_1203738_-	pfam14155, DUF4307, Domain of unknown function (DUF4307)	NA|289aa|up_4|NC_015758.1_1203839_1204706_+	TIGR03446, mycothiol_Mca, mycothiol conjugate amidase Mca	NA|89aa|up_3|NC_015758.1_1204702_1204969_+	NA	NA|674aa|up_2|NC_015758.1_1204955_1206977_+	COG1331, COG1331, Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]	NA|243aa|up_1|NC_015758.1_1207075_1207804_-	TIGR01065, Hypothetical_UPF0073_protein_yqfA	NA|263aa|up_0|NC_015758.1_1207914_1208703_+	PRK14828, PRK14828, undecaprenyl pyrophosphate synthase; Provisional	NA|107aa|down_0|NC_015758.1_1211533_1211854_+	COG0020, UppS, Undecaprenyl pyrophosphate synthase [Lipid metabolism]	NA|145aa|down_1|NC_015758.1_1212006_1212441_+	pfam00934, PE, PE family	NA|55aa|down_2|NC_015758.1_1212542_1212707_+	smart00637, CBD_II, CBD_II domain	NA|61aa|down_3|NC_015758.1_1212718_1212901_+	NA	NA|152aa|down_4|NC_015758.1_1213092_1213548_+	pfam01670, Glyco_hydro_12, Glycosyl hydrolase family 12	NA|817aa|down_5|NC_015758.1_1213962_1216413_+	pfam00934, PE, PE family	NA|313aa|down_6|NC_015758.1_1216630_1217569_-	PRK05439, PRK05439, pantothenate kinase; Provisional	NA|427aa|down_7|NC_015758.1_1217956_1219237_+	PRK00011, glyA, serine hydroxymethyltransferase; Reviewed	NA|276aa|down_8|NC_015758.1_1219341_1220169_+	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|434aa|down_9|NC_015758.1_1220379_1221681_+	COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family domains [General    function prediction only]
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	7	2087608-2087862	3	CRT	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Orphan	GCCNCCGTCGCCGCCNNTGCC	21	2	3	2087689-2087706|2087689-2087706|2087779-2087796	NC_015758.1_397827-397810|NC_015758.1_604198-604181|NC_015758.1_3429209-3429192	NA	5	5	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA|88aa|up_0|NC_015758.1_2086967_2087231_-,NA	NA|248aa|up_9|NC_015758.1_2072398_2073142_+	cd00592, HTH_MerR-like, Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators	NA|165aa|up_8|NC_015758.1_2073260_2073755_+	pfam02577, DNase-RNase, Bifunctional nuclease	NA|226aa|up_7|NC_015758.1_2074158_2074836_+	cd01105, HTH_GlnR-like, Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators	NA|942aa|up_6|NC_015758.1_2075194_2078020_+	PRK05367, PRK05367, aminomethyl-transferring glycine dehydrogenase	NA|287aa|up_5|NC_015758.1_2078246_2079107_-	PRK03204, PRK03204, haloalkane dehalogenase; Provisional	NA|289aa|up_4|NC_015758.1_2079147_2080014_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|678aa|up_3|NC_015758.1_2081921_2083955_-	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|NC_015758.1_2084074_2086300_-	PRK02999, PRK02999, malate synthase G; Provisional	NA|132aa|up_1|NC_015758.1_2086575_2086971_-	COG1848, COG1848, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]	NA|88aa|up_0|NC_015758.1_2086967_2087231_-	NA	NA|350aa|down_0|NC_015758.1_2088999_2090049_-	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]	NA|456aa|down_1|NC_015758.1_2090048_2091416_-	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]	NA|480aa|down_2|NC_015758.1_2091589_2093029_-	PRK07807, PRK07807, GuaB1 family IMP dehydrogenase-related protein	NA|484aa|down_3|NC_015758.1_2093061_2094513_-	PRK09287, PRK09287, NADP-dependent phosphogluconate dehydrogenase	NA|317aa|down_4|NC_015758.1_2094542_2095493_-	cd07326, M56_BlaR1_MecR1_like, Peptidase M56-like including those in BlaR1 and MecR1, integral membrane metallopeptidase	NA|139aa|down_5|NC_015758.1_2095507_2095924_-	COG3682, COG3682, Predicted transcriptional regulator [Transcription]	NA|141aa|down_6|NC_015758.1_2096201_2096624_+	cd03443, PaaI_thioesterase, PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria	NA|101aa|down_7|NC_015758.1_2096672_2096975_+	pfam00547, Urease_gamma, Urease, gamma subunit	NA|105aa|down_8|NC_015758.1_2096971_2097286_+	PRK13202, ureB, urease subunit beta; Reviewed	NA|578aa|down_9|NC_015758.1_2097285_2099019_+	PRK13206, ureC, urease subunit alpha; Reviewed
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	8	2169349-2169568	4	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Orphan	GTGCCAGCCGGAATCGTGATCGGCGGAACCGTCACCGACGGAATACTCA	49	0	0	NA	NA	NA	1	1	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA|136aa|up_2|NC_015758.1_2159317_2159725_-,NA|127aa|down_5|NC_015758.1_2177084_2177465_-	NA|216aa|up_9|NC_015758.1_2152631_2153279_-	pfam14081, DUF4262, Domain of unknown function (DUF4262)	NA|741aa|up_8|NC_015758.1_2153285_2155508_-	PRK15061, PRK15061, catalase/peroxidase	NA|148aa|up_7|NC_015758.1_2155545_2155989_-	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]	NA|198aa|up_6|NC_015758.1_2156102_2156696_-	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|202aa|up_5|NC_015758.1_2156778_2157384_-	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|335aa|up_4|NC_015758.1_2157483_2158488_-	cd08275, MDR3, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family	NA|251aa|up_3|NC_015758.1_2158587_2159340_+	cd16282, metallo-hydrolase-like_MBL-fold, uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain	NA|136aa|up_2|NC_015758.1_2159317_2159725_-	NA	NA|767aa|up_1|NC_015758.1_2159859_2162160_+	PLN02892, PLN02892, isocitrate lyase	NA|1839aa|up_0|NC_015758.1_2162329_2167846_-	pfam00823, PPE, PPE family	NA|155aa|down_0|NC_015758.1_2171595_2172060_-	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|NC_015758.1_2172157_2173021_+	cd07987, LPLAT_MGAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: MGAT-like	NA|424aa|down_2|NC_015758.1_2173058_2174330_-	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|372aa|down_3|NC_015758.1_2174601_2175717_+	COG1680, AmpC, Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]	NA|447aa|down_4|NC_015758.1_2175707_2177048_+	pfam00144, Beta-lactamase, Beta-lactamase	NA|127aa|down_5|NC_015758.1_2177084_2177465_-	NA	NA|621aa|down_6|NC_015758.1_2177621_2179484_+	PRK12476, PRK12476, putative fatty-acid--CoA ligase; Provisional	NA|160aa|down_7|NC_015758.1_2179491_2179971_-	pfam09167, DUF1942, Domain of unknown function (DUF1942)	NA|258aa|down_8|NC_015758.1_2180207_2180981_+	COG3361, COG3361, Uncharacterized conserved protein [Function unknown]	NA|256aa|down_9|NC_015758.1_2180984_2181752_-	PRK05867, PRK05867, SDR family oxidoreductase
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	9	3095752-3097993	2,5,4	PILER-CR,CRISPRCasFinder,CRT	no	c2c9_V-U4,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Type III-A,Type III-C,Type III-B,Type III-D	GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGA,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,NNNNNNNNGTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC	35,36,44	0	0	NA	NA	II-B,III-A:II-B,III-A:II-B,III-A	29,29,30	30	TypeIII-A,TypeIII-C,TypeIII-B,TypeIII-D	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA|85aa|up_8|NC_015758.1_3089031_3089286_-,NA|135aa|up_7|NC_015758.1_3089433_3089838_+,NA|64aa|up_6|NC_015758.1_3089834_3090026_+,NA|86aa|up_4|NC_015758.1_3091612_3091870_+,NA|104aa|up_3|NC_015758.1_3091974_3092286_+,NA|203aa|up_2|NC_015758.1_3092705_3093314_+,NA	NA|92aa|up_9|NC_015758.1_3088580_3088856_+	COG4453, COG4453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|85aa|up_8|NC_015758.1_3089031_3089286_-	NA	NA|135aa|up_7|NC_015758.1_3089433_3089838_+	NA	NA|64aa|up_6|NC_015758.1_3089834_3090026_+	NA	NA|385aa|up_5|NC_015758.1_3090224_3091379_+	pfam00665, rve, Integrase core domain	NA|86aa|up_4|NC_015758.1_3091612_3091870_+	NA	NA|104aa|up_3|NC_015758.1_3091974_3092286_+	NA	NA|203aa|up_2|NC_015758.1_3092705_3093314_+	NA	NA|470aa|up_1|NC_015758.1_3093384_3094794_+	pfam00665, rve, Integrase core domain	NA|271aa|up_0|NC_015758.1_3094790_3095603_+	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	NA|421aa|down_0|NC_015758.1_3098019_3099281_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas2|114aa|down_1|NC_015758.1_3101526_3101868_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|339aa|down_2|NC_015758.1_3101868_3102885_-	TIGR00287, CRISPR-associated_endonuclease_Cas1, CRISPR-associated endonuclease Cas1	csm5gr7|376aa|down_3|NC_015758.1_3104141_3105269_-	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm3gr7|237aa|down_4|NC_015758.1_3106154_3106865_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|125aa|down_5|NC_015758.1_3106874_3107249_-	TIGR01870, CRISPR_type_III-associated_protein_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2	cas10|813aa|down_6|NC_015758.1_3107245_3109684_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|241aa|down_7|NC_015758.1_3109680_3110403_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	NA|216aa|down_8|NC_015758.1_3110802_3111450_-	COG4293, COG4293, Uncharacterized protein conserved in bacteria [Function unknown]	NA|295aa|down_9|NC_015758.1_3111619_3112504_-	COG2253, COG2253, Uncharacterized conserved protein [Function unknown]
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	10	3099316-3101478	6,5,3	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Type III-A,Type III-C,Type III-B,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-C,TypeIII-B,TypeIII-D	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA|85aa|up_9|NC_015758.1_3089031_3089286_-,NA|135aa|up_8|NC_015758.1_3089433_3089838_+,NA|64aa|up_7|NC_015758.1_3089834_3090026_+,NA|86aa|up_5|NC_015758.1_3091612_3091870_+,NA|104aa|up_4|NC_015758.1_3091974_3092286_+,NA|203aa|up_3|NC_015758.1_3092705_3093314_+,NA	NA|85aa|up_9|NC_015758.1_3089031_3089286_-	NA	NA|135aa|up_8|NC_015758.1_3089433_3089838_+	NA	NA|64aa|up_7|NC_015758.1_3089834_3090026_+	NA	NA|385aa|up_6|NC_015758.1_3090224_3091379_+	pfam00665, rve, Integrase core domain	NA|86aa|up_5|NC_015758.1_3091612_3091870_+	NA	NA|104aa|up_4|NC_015758.1_3091974_3092286_+	NA	NA|203aa|up_3|NC_015758.1_3092705_3093314_+	NA	NA|470aa|up_2|NC_015758.1_3093384_3094794_+	pfam00665, rve, Integrase core domain	NA|271aa|up_1|NC_015758.1_3094790_3095603_+	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	NA|421aa|up_0|NC_015758.1_3098019_3099281_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas2|114aa|down_0|NC_015758.1_3101526_3101868_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	cas1|339aa|down_1|NC_015758.1_3101868_3102885_-	TIGR00287, CRISPR-associated_endonuclease_Cas1, CRISPR-associated endonuclease Cas1	csm5gr7|376aa|down_2|NC_015758.1_3104141_3105269_-	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm3gr7|237aa|down_3|NC_015758.1_3106154_3106865_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|125aa|down_4|NC_015758.1_3106874_3107249_-	TIGR01870, CRISPR_type_III-associated_protein_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2	cas10|813aa|down_5|NC_015758.1_3107245_3109684_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|241aa|down_6|NC_015758.1_3109680_3110403_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	NA|216aa|down_7|NC_015758.1_3110802_3111450_-	COG4293, COG4293, Uncharacterized protein conserved in bacteria [Function unknown]	NA|295aa|down_8|NC_015758.1_3111619_3112504_-	COG2253, COG2253, Uncharacterized conserved protein [Function unknown]	NA|296aa|down_9|NC_015758.1_3112506_3113394_-	pfam09407, AbiEi_1, AbiEi antitoxin C-terminal domain
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	11	3831520-3831609	7	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Orphan	CCAGGCGTTGGGCTGGCTGCCGAT	24	0	0	NA	NA	NA	1	1	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA|77aa|up_7|NC_015758.1_3824914_3825145_+,NA|121aa|up_6|NC_015758.1_3825248_3825611_-,NA|73aa|up_2|NC_015758.1_3829585_3829804_-,NA|121aa|down_0|NC_015758.1_3832594_3832957_-,NA|52aa|down_2|NC_015758.1_3834798_3834954_-,NA|52aa|down_3|NC_015758.1_3834978_3835134_-,NA|238aa|down_6|NC_015758.1_3839169_3839883_-	NA|169aa|up_9|NC_015758.1_3823225_3823732_-	COG0802, COG0802, Predicted ATPase or kinase [General function prediction only]	NA|409aa|up_8|NC_015758.1_3823728_3824955_-	PRK00053, alr, alanine racemase; Reviewed	NA|77aa|up_7|NC_015758.1_3824914_3825145_+	NA	NA|121aa|up_6|NC_015758.1_3825248_3825611_-	NA	NA|177aa|up_5|NC_015758.1_3825773_3826304_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|177aa|up_4|NC_015758.1_3826570_3827101_+	pfam00823, PPE, PPE family	NA|725aa|up_3|NC_015758.1_3827418_3829593_-	COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair]	NA|73aa|up_2|NC_015758.1_3829585_3829804_-	NA	NA|100aa|up_1|NC_015758.1_3830298_3830598_+	pfam00934, PE, PE family	NA|181aa|up_0|NC_015758.1_3830683_3831226_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|121aa|down_0|NC_015758.1_3832594_3832957_-	NA	NA|179aa|down_1|NC_015758.1_3833119_3833656_+	pfam00823, PPE, PPE family	NA|52aa|down_2|NC_015758.1_3834798_3834954_-	NA	NA|52aa|down_3|NC_015758.1_3834978_3835134_-	NA	NA|461aa|down_4|NC_015758.1_3836326_3837709_-	TIGR01788, Glutamate_decarboxylase_alpha_GAD-alpha	NA|474aa|down_5|NC_015758.1_3837746_3839168_-	pfam01256, Carb_kinase, Carbohydrate kinase	NA|238aa|down_6|NC_015758.1_3839169_3839883_-	NA	NA|285aa|down_7|NC_015758.1_3839893_3840748_-	pfam14494, DUF4436, Domain of unknown function (DUF4436)	NA|625aa|down_8|NC_015758.1_3840969_3842844_-	PRK00331, PRK00331, isomerizing glutamine--fructose-6-phosphate transaminase	NA|159aa|down_9|NC_015758.1_3842865_3843342_+	pfam10708, DUF2510, Protein of unknown function (DUF2510)
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	12	3930562-3930797	4	PILER-CR	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Orphan	CACCGGCGGAGCCGGCGGGGCCGGCGGGGCCGGCGGTAACAGCGGAGCCGGCG	53	2	3	3930615-3930659|3930615-3930659|3930713-3930763	NC_015758.1_3930949-3930993|NC_015758.1_3931234-3931278|NC_015758.1_3931323-3931373	NA	2	2	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA,NA|280aa|down_2|NC_015758.1_3935283_3936123_+	NA|64aa|up_9|NC_015758.1_3906661_3906853_-	COG1141, Fer, Ferredoxin [Energy production and conversion]	NA|401aa|up_8|NC_015758.1_3907067_3908270_+	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|374aa|up_7|NC_015758.1_3908294_3909416_+	COG1960, CaiA, Acyl-CoA dehydrogenases [Lipid metabolism]	NA|503aa|up_6|NC_015758.1_3909486_3910995_+	PRK07867, PRK07867, acyl-CoA synthetase; Validated	NA|1427aa|up_5|NC_015758.1_3911165_3915446_+	pfam00934, PE, PE family	NA|516aa|up_4|NC_015758.1_3920466_3922014_-	PRK07586, PRK07586, acetolactate synthase large subunit	NA|279aa|up_3|NC_015758.1_3922010_3922847_-	COG2159, COG2159, Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only]	NA|126aa|up_2|NC_015758.1_3925355_3925733_+	PRK12270, kgd, multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit	NA|669aa|up_1|NC_015758.1_3925766_3927773_+	PRK07764, PRK07764, DNA polymerase III subunits gamma and tau; Validated	NA|219aa|up_0|NC_015758.1_3928788_3929445_-	PRK07798, PRK07798, acyl-CoA synthetase; Validated	NA|549aa|down_0|NC_015758.1_3932676_3934323_-	PRK07798, PRK07798, acyl-CoA synthetase; Validated	NA|264aa|down_1|NC_015758.1_3934396_3935188_+	PRK07799, PRK07799, crotonase/enoyl-CoA hydratase family protein	NA|280aa|down_2|NC_015758.1_3935283_3936123_+	NA	NA|237aa|down_3|NC_015758.1_3937401_3938112_+	pfam06314, ADC, Acetoacetate decarboxylase (ADC)	NA|348aa|down_4|NC_015758.1_3938176_3939220_-	TIGR03559, F420_Rv3520c, probable F420-dependent oxidoreductase, Rv3520c family	NA|304aa|down_5|NC_015758.1_3939372_3940284_+	COG1545, COG1545, Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]	NA|355aa|down_6|NC_015758.1_3940299_3941364_+	PRK07937, PRK07937, lipid-transfer protein; Provisional	NA|395aa|down_7|NC_015758.1_3941380_3942565_+	PRK08313, PRK08313, thiolase domain-containing protein	NA|344aa|down_8|NC_015758.1_3942606_3943638_+	cd14952, NHL_PKND_like, NHL repeat domain of the protein kinase PknD	NA|175aa|down_9|NC_015758.1_3943651_3944176_-	COG0663, PaaY, Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily [General function prediction only]
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	13	4070071-4070290	5	PILER-CR	no	cas3	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	Unclear	GCTATTCGGCGCCGGCGGCGCCGGCGGCGCCGGCGGG	37	0	0	NA	NA	NA	2	2	Unclear	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,csm3gr7,csm2gr11,cas10,cas6	NA|64aa|up_9|NC_015758.1_4056973_4057165_+,NA|193aa|up_5|NC_015758.1_4063423_4064002_-,NA|52aa|up_0|NC_015758.1_4068834_4068990_-,NA|100aa|down_1|NC_015758.1_4070941_4071241_-,NA|257aa|down_8|NC_015758.1_4077204_4077975_-	NA|64aa|up_9|NC_015758.1_4056973_4057165_+	NA	NA|402aa|up_8|NC_015758.1_4057329_4058535_-	PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated	NA|550aa|up_7|NC_015758.1_4058620_4060270_+	cd07302, CHD, cyclase homology domain	NA|935aa|up_6|NC_015758.1_4060266_4063071_-	PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated	NA|193aa|up_5|NC_015758.1_4063423_4064002_-	NA	NA|68aa|up_4|NC_015758.1_4064141_4064345_-	COG1278, CspC, Cold shock proteins [Transcription]	cas3|772aa|up_3|NC_015758.1_4064594_4066910_+	TIGR03817, DECH_helic, helicase/secretion neighborhood putative DEAH-box helicase	NA|95aa|up_2|NC_015758.1_4067046_4067331_+	pfam00934, PE, PE family	NA|346aa|up_1|NC_015758.1_4067654_4068692_+	pfam18621, DUF5628, Family of unknown function (DUF5628)	NA|52aa|up_0|NC_015758.1_4068834_4068990_-	NA	NA|126aa|down_0|NC_015758.1_4070601_4070979_-	TIGR03816, tadE_like_DECH, helicase/secretion neighborhood TadE-like protein	NA|100aa|down_1|NC_015758.1_4070941_4071241_-	NA	NA|69aa|down_2|NC_015758.1_4071264_4071471_-	pfam14029, DUF4244, Protein of unknown function (DUF4244)	NA|192aa|down_3|NC_015758.1_4071480_4072056_-	COG2064, TadC, Flp pilus assembly protein TadC [Cell motility and secretion / Intracellular trafficking and secretion]	NA|267aa|down_4|NC_015758.1_4072079_4072880_-	COG4965, TadB, Flp pilus assembly protein TadB [Intracellular trafficking and secretion]	NA|388aa|down_5|NC_015758.1_4072876_4074040_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|351aa|down_6|NC_015758.1_4074036_4075089_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|288aa|down_7|NC_015758.1_4075586_4076450_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|257aa|down_8|NC_015758.1_4077204_4077975_-	NA	NA|549aa|down_9|NC_015758.1_4077971_4079618_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]
GCF_000253355.1_ASM25335v1	NC_015758	Mycobacterium tuberculosis variant africanum GM041182, complete genome	14	4086618-4086706	8	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,cas1,csm5gr7,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,csm3gr7,csm2gr11,cas10,cas6	NA|257aa|up_6|NC_015758.1_4077204_4077975_-,NA|233aa|up_0|NC_015758.1_4085722_4086421_-,NA|126aa|down_6|NC_015758.1_4091941_4092319_+	NA|388aa|up_9|NC_015758.1_4072876_4074040_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|351aa|up_8|NC_015758.1_4074036_4075089_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|288aa|up_7|NC_015758.1_4075586_4076450_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|257aa|up_6|NC_015758.1_4077204_4077975_-	NA	NA|549aa|up_5|NC_015758.1_4077971_4079618_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]	NA|288aa|up_4|NC_015758.1_4079614_4080478_-	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|NC_015758.1_4080470_4081397_-	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|NC_015758.1_4081398_4083024_-	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|NC_015758.1_4083731_4085687_+	PRK00174, PRK00174, acetyl-CoA synthetase; Provisional	NA|233aa|up_0|NC_015758.1_4085722_4086421_-	NA	NA|173aa|down_0|NC_015758.1_4086766_4087285_+	pfam07332, Phage_holin_3_6, Putative Actinobacterial Holin-X, holin superfamily III	NA|328aa|down_1|NC_015758.1_4087285_4088269_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|398aa|down_2|NC_015758.1_4088261_4089455_-	pfam13365, Trypsin_2, Trypsin-like peptidase domain	NA|274aa|down_3|NC_015758.1_4089460_4090282_-	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|NC_015758.1_4090413_4091097_-	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins	NA|246aa|down_5|NC_015758.1_4091096_4091834_-	COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]	NA|126aa|down_6|NC_015758.1_4091941_4092319_+	NA	NA|225aa|down_7|NC_015758.1_4092417_4093092_+	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]	NA|265aa|down_8|NC_015758.1_4093197_4093992_-	cd16278, metallo-hydrolase-like_MBL-fold, uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain	NA|152aa|down_9|NC_015758.1_4093998_4094454_-	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
