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_902459825.1_MB3601_COMBINED	NZ_LR699570	Mycobacterium tuberculosis variant bovis strain Mb3601 isolate 14Z005608 chromosome Mb3601	1	331998-332109	1	PILER-CR	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	CCGCCGTTGCCGCCGTTGCCGATCA	25	1	5	332068-332084|332068-332084|332068-332084|332068-332084|332068-332084	NZ_LR699570.1_1189303-1189319|NZ_LR699570.1_2415605-2415621|NZ_LR699570.1_2782431-2782447|NZ_LR699570.1_3995668-3995684|NZ_LR699570.1_841640-841624	NA	2	2	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|61aa|up_0|NZ_LR699570.1_330331_330514_-,NA	NA|398aa|up_9|NZ_LR699570.1_320509_321703_-	COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]	NA|561aa|up_8|NZ_LR699570.1_321738_323421_+	PRK07788, PRK07788, acyl-CoA synthetase; Validated	NA|732aa|up_7|NZ_LR699570.1_323437_325633_-	cd01152, ACAD_fadE6_17_26, Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26	NA|378aa|up_6|NZ_LR699570.1_325746_326880_-	pfam12146, Hydrolase_4, Serine aminopeptidase, S33	NA|207aa|up_5|NZ_LR699570.1_326876_327497_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|194aa|up_4|NZ_LR699570.1_327593_328175_+	pfam00903, Glyoxalase, Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily	NA|242aa|up_3|NZ_LR699570.1_328104_328830_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|307aa|up_2|NZ_LR699570.1_328919_329840_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	NA|143aa|up_1|NZ_LR699570.1_329879_330308_-	cd18678, PIN_MtVapC25_VapC33-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins	NA|61aa|up_0|NZ_LR699570.1_330331_330514_-	NA	NA|900aa|down_0|NZ_LR699570.1_333687_336387_-	pfam00934, PE, PE family	NA|838aa|down_1|NZ_LR699570.1_336636_339150_-	pfam00934, PE, PE family	NA|537aa|down_2|NZ_LR699570.1_339440_341051_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|303aa|down_3|NZ_LR699570.1_341074_341983_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|632aa|down_4|NZ_LR699570.1_342206_344102_+	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA	NA|539aa|down_5|NZ_LR699570.1_344098_345715_+	pfam05108, T7SS_ESX1_EccB, Type VII secretion system ESX-1, transport TM domain B	NA|1331aa|down_6|NZ_LR699570.1_345711_349704_+	TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa	NA|103aa|down_7|NZ_LR699570.1_349700_350009_+	pfam00934, PE, PE family	NA|514aa|down_8|NZ_LR699570.1_350011_351553_+	COG5651, COG5651, PPE-repeat proteins [Cell motility and secretion]	NA|98aa|down_9|NZ_LR699570.1_351601_351895_+	TIGR03930, WXG100_ESAT6, WXG100 family type VII secretion target
GCF_902459825.1_MB3601_COMBINED	NZ_LR699570	Mycobacterium tuberculosis variant bovis strain Mb3601 isolate 14Z005608 chromosome Mb3601	2	692073-692149	1	CRISPRCasFinder	no	c2c9_V-U4	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,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,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA	NA|229aa|up_9|NZ_LR699570.1_678434_679121_-	pfam10738, Lpp-LpqN, Probable lipoprotein LpqN	NA|878aa|up_8|NZ_LR699570.1_679274_681908_+	COG3537, COG3537, Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]	NA|796aa|up_7|NZ_LR699570.1_681930_684318_-	pfam03706, LPG_synthase_TM, Lysylphosphatidylglycerol synthase TM region	NA|241aa|up_6|NZ_LR699570.1_684455_685178_+	COG2186, FadR, Transcriptional regulators [Transcription]	NA|266aa|up_5|NZ_LR699570.1_685174_685972_+	COG0767, Ttg2B, ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|296aa|up_4|NZ_LR699570.1_685973_686861_+	COG0767, Ttg2B, ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|405aa|up_3|NZ_LR699570.1_686866_688081_+	pfam11887, Mce4_CUP1, Cholesterol uptake porter CUP1 of Mce4, putative	NA|344aa|up_2|NZ_LR699570.1_688077_689109_+	COG1463, Ttg2C, ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]	NA|482aa|up_1|NZ_LR699570.1_689105_690551_+	TIGR00996, Mtu_fam_mce, virulence factor Mce family protein	NA|479aa|up_0|NZ_LR699570.1_690547_691984_+	TIGR00996, Mtu_fam_mce, virulence factor Mce family protein	NA|517aa|down_0|NZ_LR699570.1_693284_694835_+	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_LR699570.1_694886_695279_-	cd18768, PIN_MtVapC4-C5-like, VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins	NA|86aa|down_2|NZ_LR699570.1_695275_695533_-	COG4118, Phd, Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]	NA|412aa|down_3|NZ_LR699570.1_695715_696951_-	COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General function prediction only]	NA|138aa|down_4|NZ_LR699570.1_697201_697615_-	cd18681, PIN_MtVapC27-VapC40_like, VapC-like PIN domain of Mycobacterium tuberculosis VapC27, and VapC40, and related proteins	NA|79aa|down_5|NZ_LR699570.1_697611_697848_-	COG2002, AbrB, Regulators of stationary/sporulation gene expression [Transcription]	NA|169aa|down_6|NZ_LR699570.1_697951_698458_-	COG0642, BaeS, Signal transduction histidine kinase [Signal transduction mechanisms]	NA|157aa|down_7|NZ_LR699570.1_698571_699042_-	PRK10755, PRK10755, two-component system sensor histidine kinase PmrB	NA|254aa|down_8|NZ_LR699570.1_699085_699847_-	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_LR699570.1_699903_700215_+	pfam03413, PepSY, Peptidase propeptide and YPEB domain
GCF_902459825.1_MB3601_COMBINED	NZ_LR699570	Mycobacterium tuberculosis variant bovis strain Mb3601 isolate 14Z005608 chromosome Mb3601	3	926250-927161	1	CRT	no	csa3	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type I-A	CGGGGCCGGCGGGGCCGGCGG	21	1	22	927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143|927117-927143	NZ_LR699570.1_834129-834155|NZ_LR699570.1_840379-840405|NZ_LR699570.1_841705-841731|NZ_LR699570.1_925983-926009|NZ_LR699570.1_330788-330762|NZ_LR699570.1_333802-333776|NZ_LR699570.1_336748-336722|NZ_LR699570.1_2415810-2415784|NZ_LR699570.1_837501-837527|NZ_LR699570.1_838599-838625|NZ_LR699570.1_925884-925910|NZ_LR699570.1_1214356-1214382|NZ_LR699570.1_3769451-3769477|NZ_LR699570.1_3899387-3899413|NZ_LR699570.1_3899543-3899569|NZ_LR699570.1_334753-334727|NZ_LR699570.1_335092-335066|NZ_LR699570.1_337867-337841|NZ_LR699570.1_675174-675148|NZ_LR699570.1_1657440-1657414|NZ_LR699570.1_1854911-1854885|NZ_LR699570.1_2060654-2060628	NA	19	19	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA,NA|184aa|down_2|NZ_LR699570.1_931279_931831_-,NA|81aa|down_8|NZ_LR699570.1_937312_937555_+	NA|685aa|up_9|NZ_LR699570.1_913885_915940_-	TIGR00350, Transcriptional_regulator_LytR, cell envelope-related function transcriptional attenuator common domain	NA|390aa|up_8|NZ_LR699570.1_916105_917275_-	TIGR00737, Probable_tRNA-dihydrouridine_synthase, putative TIM-barrel protein, nifR3 family	NA|339aa|up_7|NZ_LR699570.1_917362_918379_-	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|214aa|up_6|NZ_LR699570.1_918540_919182_-	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|352aa|up_5|NZ_LR699570.1_919262_920318_+	COG3662, COG3662, Uncharacterized protein conserved in bacteria [Function unknown]	csa3|131aa|up_4|NZ_LR699570.1_920369_920762_-	smart00418, HTH_ARSR, helix_turn_helix, Arsenical Resistance Operon Repressor	NA|141aa|up_3|NZ_LR699570.1_920819_921242_-	COG0590, CumB, Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]	NA|97aa|up_2|NZ_LR699570.1_921203_921494_+	COG0675, COG0675, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|302aa|up_1|NZ_LR699570.1_921598_922504_+	COG3315, COG3315, O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]	NA|272aa|up_0|NZ_LR699570.1_922522_923338_-	TIGR04255, hypothetical_protein, TIGR04255 family protein	NA|883aa|down_0|NZ_LR699570.1_927538_930187_-	pfam00934, PE, PE family	NA|215aa|down_1|NZ_LR699570.1_930654_931299_+	pfam14032, PknH_C, PknH-like extracellular domain	NA|184aa|down_2|NZ_LR699570.1_931279_931831_-	NA	NA|241aa|down_3|NZ_LR699570.1_931911_932634_-	COG4849, COG4849, Predicted nucleotidyltransferase [General function prediction    only]	NA|343aa|down_4|NZ_LR699570.1_932704_933733_-	COG4861, COG4861, Uncharacterized protein conserved in bacteria [Function unknown]	NA|263aa|down_5|NZ_LR699570.1_934421_935210_+	pfam01427, Peptidase_M15, D-ala-D-ala dipeptidase	NA|271aa|down_6|NZ_LR699570.1_935296_936109_+	pfam13847, Methyltransf_31, Methyltransferase domain	NA|287aa|down_7|NZ_LR699570.1_936176_937037_-	TIGR01250, Proline_iminopeptidase, proline-specific peptidase, Bacillus coagulans-type subfamily	NA|81aa|down_8|NZ_LR699570.1_937312_937555_+	NA	NA|431aa|down_9|NZ_LR699570.1_937831_939124_+	cd17329, MFS_MdtH_MDR_like, Multidrug resistance protein MdtH and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily
GCF_902459825.1_MB3601_COMBINED	NZ_LR699570	Mycobacterium tuberculosis variant bovis strain Mb3601 isolate 14Z005608 chromosome Mb3601	4	1212563-1213380	2	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	GGCGGTGTCGGCGGTGCCGGCGG	23	6	88	1212664-1212679|1212817-1212838|1212862-1212877|1213000-1213021|1213000-1213021|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213117-1213135|1213291-1213312|1213291-1213312|1213291-1213312|1213291-1213312	NZ_LR699570.1_2416005-2415990|NZ_LR699570.1_2938458-2938437|NZ_LR699570.1_2087788-2087773|NZ_LR699570.1_837963-837984|NZ_LR699570.1_1218251-1218272|NZ_LR699570.1_840212-840230|NZ_LR699570.1_1218224-1218242|NZ_LR699570.1_1218296-1218314|NZ_LR699570.1_334189-334171|NZ_LR699570.1_674838-674820|NZ_LR699570.1_1631980-1631962|NZ_LR699570.1_1634806-1634788|NZ_LR699570.1_1637651-1637633|NZ_LR699570.1_1638413-1638395|NZ_LR699570.1_1989121-1989103|NZ_LR699570.1_2060828-2060810|NZ_LR699570.1_2061374-2061356|NZ_LR699570.1_2779353-2779335|NZ_LR699570.1_2782876-2782858|NZ_LR699570.1_149039-149057|NZ_LR699570.1_338505-338523|NZ_LR699570.1_624029-624047|NZ_LR699570.1_624251-624269|NZ_LR699570.1_841207-841225|NZ_LR699570.1_1090673-1090691|NZ_LR699570.1_1091321-1091339|NZ_LR699570.1_1213489-1213507|NZ_LR699570.1_1213996-1214014|NZ_LR699570.1_1214245-1214263|NZ_LR699570.1_1214263-1214281|NZ_LR699570.1_1218542-1218560|NZ_LR699570.1_2000716-2000734|NZ_LR699570.1_2411740-2411758|NZ_LR699570.1_2672011-2672029|NZ_LR699570.1_3021615-3021633|NZ_LR699570.1_3021714-3021732|NZ_LR699570.1_3672848-3672866|NZ_LR699570.1_3768032-3768050|NZ_LR699570.1_3768215-3768233|NZ_LR699570.1_3889582-3889600|NZ_LR699570.1_3891321-3891339|NZ_LR699570.1_3891975-3891993|NZ_LR699570.1_3899765-3899783|NZ_LR699570.1_4047097-4047115|NZ_LR699570.1_4047187-4047205|NZ_LR699570.1_4047295-4047313|NZ_LR699570.1_330953-330935|NZ_LR699570.1_332180-332162|NZ_LR699570.1_335296-335278|NZ_LR699570.1_335749-335731|NZ_LR699570.1_335800-335782|NZ_LR699570.1_335809-335791|NZ_LR699570.1_338080-338062|NZ_LR699570.1_338209-338191|NZ_LR699570.1_338476-338458|NZ_LR699570.1_338599-338581|NZ_LR699570.1_363130-363112|NZ_LR699570.1_443372-443354|NZ_LR699570.1_546725-546707|NZ_LR699570.1_674004-673986|NZ_LR699570.1_1095391-1095373|NZ_LR699570.1_1490844-1490826|NZ_LR699570.1_1619946-1619928|NZ_LR699570.1_1620399-1620381|NZ_LR699570.1_1637516-1637498|NZ_LR699570.1_1637525-1637507|NZ_LR699570.1_1637738-1637720|NZ_LR699570.1_1637789-1637771|NZ_LR699570.1_1854488-1854470|NZ_LR699570.1_1855016-1854998|NZ_LR699570.1_1988395-1988377|NZ_LR699570.1_2087986-2087968|NZ_LR699570.1_2299023-2299005|NZ_LR699570.1_2350414-2350396|NZ_LR699570.1_2415723-2415705|NZ_LR699570.1_2558407-2558389|NZ_LR699570.1_2772669-2772651|NZ_LR699570.1_2773251-2773233|NZ_LR699570.1_3705356-3705338|NZ_LR699570.1_3705980-3705962|NZ_LR699570.1_3706223-3706205|NZ_LR699570.1_3706355-3706337|NZ_LR699570.1_3708260-3708242|NZ_LR699570.1_3990438-3990420|NZ_LR699570.1_623921-623942|NZ_LR699570.1_36710-36689|NZ_LR699570.1_130978-130999|NZ_LR699570.1_2900202-2900223	NA	16	16	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|89aa|up_3|NZ_LR699570.1_1207995_1208262_+,NA|61aa|down_3|NZ_LR699570.1_1215831_1216014_+	NA|465aa|up_9|NZ_LR699570.1_1202329_1203724_+	TIGR01137, Cystathionine_beta-synthase, cystathionine beta-synthase	NA|241aa|up_8|NZ_LR699570.1_1203925_1204648_+	pfam06271, RDD, RDD family	NA|389aa|up_7|NZ_LR699570.1_1204679_1205846_+	PRK07811, PRK07811, cystathionine gamma-synthase; Provisional	NA|165aa|up_6|NZ_LR699570.1_1205916_1206411_-	PRK00226, greA, transcription elongation factor GreA; Reviewed	NA|145aa|up_5|NZ_LR699570.1_1206596_1207031_-	pfam14155, DUF4307, Domain of unknown function (DUF4307)	NA|289aa|up_4|NZ_LR699570.1_1207132_1207999_+	TIGR03446, mycothiol_Mca, mycothiol conjugate amidase Mca	NA|89aa|up_3|NZ_LR699570.1_1207995_1208262_+	NA	NA|674aa|up_2|NZ_LR699570.1_1208248_1210270_+	COG1331, COG1331, Highly conserved protein containing a thioredoxin domain [Posttranslational modification, protein turnover, chaperones]	NA|243aa|up_1|NZ_LR699570.1_1210368_1211097_-	TIGR01065, Hypothetical_UPF0073_protein_yqfA	NA|263aa|up_0|NZ_LR699570.1_1211207_1211996_+	PRK14828, PRK14828, undecaprenyl pyrophosphate synthase; Provisional	NA|107aa|down_0|NZ_LR699570.1_1214646_1214967_+	COG0020, UppS, Undecaprenyl pyrophosphate synthase [Lipid metabolism]	NA|145aa|down_1|NZ_LR699570.1_1215119_1215554_+	pfam00934, PE, PE family	NA|55aa|down_2|NZ_LR699570.1_1215655_1215820_+	smart00637, CBD_II, CBD_II domain	NA|61aa|down_3|NZ_LR699570.1_1215831_1216014_+	NA	NA|152aa|down_4|NZ_LR699570.1_1216205_1216661_+	pfam01670, Glyco_hydro_12, Glycosyl hydrolase family 12	NA|817aa|down_5|NZ_LR699570.1_1217075_1219526_+	pfam00934, PE, PE family	NA|313aa|down_6|NZ_LR699570.1_1219743_1220682_-	PRK05439, PRK05439, pantothenate kinase; Provisional	NA|427aa|down_7|NZ_LR699570.1_1221069_1222350_+	PRK00011, glyA, serine hydroxymethyltransferase; Reviewed	NA|276aa|down_8|NZ_LR699570.1_1222454_1223282_+	cd01050, Acyl_ACP_Desat, Acyl ACP desaturase, ferritin-like diiron-binding domain	NA|434aa|down_9|NZ_LR699570.1_1223492_1224794_+	COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family domains [General    function prediction only]
GCF_902459825.1_MB3601_COMBINED	NZ_LR699570	Mycobacterium tuberculosis variant bovis strain Mb3601 isolate 14Z005608 chromosome Mb3601	5	2087458-2087712	2	CRT	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Orphan	GCCNCCGTCGCCGCCNNTGCC	21	2	3	2087539-2087556|2087539-2087556|2087629-2087646	NZ_LR699570.1_401138-401121|NZ_LR699570.1_607391-607374|NZ_LR699570.1_3419623-3419606	NA	5	5	Orphan	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|88aa|up_0|NZ_LR699570.1_2086817_2087081_-,NA	NA|165aa|up_9|NZ_LR699570.1_2073223_2073718_+	pfam02577, DNase-RNase, Bifunctional nuclease	NA|226aa|up_8|NZ_LR699570.1_2074009_2074687_+	cd01105, HTH_GlnR-like, Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators	NA|942aa|up_7|NZ_LR699570.1_2075045_2077871_+	PRK05367, PRK05367, aminomethyl-transferring glycine dehydrogenase	NA|287aa|up_6|NZ_LR699570.1_2078097_2078958_-	PRK03204, PRK03204, haloalkane dehalogenase; Provisional	NA|289aa|up_5|NZ_LR699570.1_2078998_2079865_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|629aa|up_4|NZ_LR699570.1_2079869_2081756_-	TIGR00976, Hypothetical_protein_Rv1835c/MT1883/Mb1866c	NA|678aa|up_3|NZ_LR699570.1_2081771_2083805_-	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_LR699570.1_2083924_2086150_-	PRK02999, PRK02999, malate synthase G; Provisional	NA|132aa|up_1|NZ_LR699570.1_2086425_2086821_-	COG1848, COG1848, Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]	NA|88aa|up_0|NZ_LR699570.1_2086817_2087081_-	NA	NA|350aa|down_0|NZ_LR699570.1_2088848_2089898_-	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]	NA|456aa|down_1|NZ_LR699570.1_2089897_2091265_-	COG1253, TlyC, Hemolysins and related proteins containing CBS domains [General function prediction only]	NA|480aa|down_2|NZ_LR699570.1_2091438_2092878_-	PRK07807, PRK07807, GuaB1 family IMP dehydrogenase-related protein	NA|317aa|down_3|NZ_LR699570.1_2094390_2095341_-	cd07326, M56_BlaR1_MecR1_like, Peptidase M56-like including those in BlaR1 and MecR1, integral membrane metallopeptidase	NA|139aa|down_4|NZ_LR699570.1_2095355_2095772_-	COG3682, COG3682, Predicted transcriptional regulator [Transcription]	NA|141aa|down_5|NZ_LR699570.1_2096049_2096472_+	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_LR699570.1_2096520_2096823_+	pfam00547, Urease_gamma, Urease, gamma subunit	NA|105aa|down_7|NZ_LR699570.1_2096819_2097134_+	PRK13202, ureB, urease subunit beta; Reviewed	NA|578aa|down_8|NZ_LR699570.1_2097133_2098867_+	PRK13206, ureC, urease subunit alpha; Reviewed	NA|212aa|down_9|NZ_LR699570.1_2098866_2099502_+	COG0830, UreF, Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]
GCF_902459825.1_MB3601_COMBINED	NZ_LR699570	Mycobacterium tuberculosis variant bovis strain Mb3601 isolate 14Z005608 chromosome Mb3601	6	2169329-2169454	3	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,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,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|136aa|up_2|NZ_LR699570.1_2159163_2159571_-,NA|127aa|down_5|NZ_LR699570.1_2177063_2177444_-	NA|216aa|up_9|NZ_LR699570.1_2152477_2153125_-	pfam14081, DUF4262, Domain of unknown function (DUF4262)	NA|741aa|up_8|NZ_LR699570.1_2153131_2155354_-	PRK15061, PRK15061, catalase/peroxidase	NA|148aa|up_7|NZ_LR699570.1_2155391_2155835_-	COG0735, Fur, Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]	NA|198aa|up_6|NZ_LR699570.1_2155948_2156542_-	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|202aa|up_5|NZ_LR699570.1_2156624_2157230_-	COG1881, COG1881, Phospholipid-binding protein [General function prediction only]	NA|335aa|up_4|NZ_LR699570.1_2157329_2158334_-	cd08275, MDR3, Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family	NA|251aa|up_3|NZ_LR699570.1_2158433_2159186_+	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_LR699570.1_2159163_2159571_-	NA	NA|767aa|up_1|NZ_LR699570.1_2159705_2162006_+	PLN02892, PLN02892, isocitrate lyase	NA|1883aa|up_0|NZ_LR699570.1_2162175_2167824_-	pfam00823, PPE, PPE family	NA|155aa|down_0|NZ_LR699570.1_2171574_2172039_-	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_LR699570.1_2172136_2173000_+	cd07987, LPLAT_MGAT-like, Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: MGAT-like	NA|424aa|down_2|NZ_LR699570.1_2173037_2174309_-	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|372aa|down_3|NZ_LR699570.1_2174580_2175696_+	COG1680, AmpC, Beta-lactamase class C and other penicillin binding proteins [Defense mechanisms]	NA|447aa|down_4|NZ_LR699570.1_2175686_2177027_+	pfam00144, Beta-lactamase, Beta-lactamase	NA|127aa|down_5|NZ_LR699570.1_2177063_2177444_-	NA	NA|621aa|down_6|NZ_LR699570.1_2177600_2179463_+	PRK12476, PRK12476, putative fatty-acid--CoA ligase; Provisional	NA|160aa|down_7|NZ_LR699570.1_2179470_2179950_-	pfam09167, DUF1942, Domain of unknown function (DUF1942)	NA|258aa|down_8|NZ_LR699570.1_2180186_2180960_+	COG3361, COG3361, Uncharacterized conserved protein [Function unknown]	NA|256aa|down_9|NZ_LR699570.1_2180963_2181731_-	PRK05867, PRK05867, SDR family oxidoreductase
GCF_902459825.1_MB3601_COMBINED	NZ_LR699570	Mycobacterium tuberculosis variant bovis strain Mb3601 isolate 14Z005608 chromosome Mb3601	7	3086144-3087355	2,4,3	PILER-CR,CRISPRCasFinder,CRT	no	c2c9_V-U4,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type III-D,Type III-C,Type III-B,Type III-A	GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC,GTTTCCGTCCCCTCTCGGGGTTTTGGGTCTGACGAC	36,36,36	1	1	3086847-3086881	NZ_LR699570.1_3087356-3087390	II-B,III-A:II-B,III-A:II-B,III-A	16,16,16	16	TypeIII-D,TypeIII-C,TypeIII-B,TypeIII-A	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|85aa|up_8|NZ_LR699570.1_3079423_3079678_-,NA|135aa|up_7|NZ_LR699570.1_3079825_3080230_+,NA|64aa|up_6|NZ_LR699570.1_3080226_3080418_+,NA|86aa|up_4|NZ_LR699570.1_3082004_3082262_+,NA|104aa|up_3|NZ_LR699570.1_3082366_3082678_+,NA|203aa|up_2|NZ_LR699570.1_3083097_3083706_+,NA	NA|92aa|up_9|NZ_LR699570.1_3078972_3079248_+	COG4453, COG4453, Uncharacterized protein conserved in bacteria [Function unknown]	NA|85aa|up_8|NZ_LR699570.1_3079423_3079678_-	NA	NA|135aa|up_7|NZ_LR699570.1_3079825_3080230_+	NA	NA|64aa|up_6|NZ_LR699570.1_3080226_3080418_+	NA	NA|385aa|up_5|NZ_LR699570.1_3080616_3081771_+	pfam00665, rve, Integrase core domain	NA|86aa|up_4|NZ_LR699570.1_3082004_3082262_+	NA	NA|104aa|up_3|NZ_LR699570.1_3082366_3082678_+	NA	NA|203aa|up_2|NZ_LR699570.1_3083097_3083706_+	NA	NA|470aa|up_1|NZ_LR699570.1_3083776_3085186_+	pfam00665, rve, Integrase core domain	NA|271aa|up_0|NZ_LR699570.1_3085182_3085995_+	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	NA|421aa|down_0|NZ_LR699570.1_3087452_3088714_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas2|114aa|down_1|NZ_LR699570.1_3090967_3091309_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	NA|421aa|down_2|NZ_LR699570.1_3092046_3093308_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	csm5gr7|376aa|down_3|NZ_LR699570.1_3094940_3096068_-	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm4gr5|303aa|down_4|NZ_LR699570.1_3096064_3096973_-	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm3gr7|237aa|down_5|NZ_LR699570.1_3096953_3097664_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|125aa|down_6|NZ_LR699570.1_3097673_3098048_-	TIGR01870, CRISPR_type_III-associated_protein_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2	cas10|813aa|down_7|NZ_LR699570.1_3098044_3100483_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|241aa|down_8|NZ_LR699570.1_3100479_3101202_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	NA|182aa|down_9|NZ_LR699570.1_3101601_3102147_-	COG4293, COG4293, Uncharacterized protein conserved in bacteria [Function unknown]
GCF_902459825.1_MB3601_COMBINED	NZ_LR699570	Mycobacterium tuberculosis variant bovis strain Mb3601 isolate 14Z005608 chromosome Mb3601	8	3088749-3090919	5,4,3	CRISPRCasFinder,CRT,PILER-CR	no	cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	Type III-D,Type III-C,Type III-B,Type III-A	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-D,TypeIII-C,TypeIII-B,TypeIII-A	RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|85aa|up_9|NZ_LR699570.1_3079423_3079678_-,NA|135aa|up_8|NZ_LR699570.1_3079825_3080230_+,NA|64aa|up_7|NZ_LR699570.1_3080226_3080418_+,NA|86aa|up_5|NZ_LR699570.1_3082004_3082262_+,NA|104aa|up_4|NZ_LR699570.1_3082366_3082678_+,NA|203aa|up_3|NZ_LR699570.1_3083097_3083706_+,NA	NA|85aa|up_9|NZ_LR699570.1_3079423_3079678_-	NA	NA|135aa|up_8|NZ_LR699570.1_3079825_3080230_+	NA	NA|64aa|up_7|NZ_LR699570.1_3080226_3080418_+	NA	NA|385aa|up_6|NZ_LR699570.1_3080616_3081771_+	pfam00665, rve, Integrase core domain	NA|86aa|up_5|NZ_LR699570.1_3082004_3082262_+	NA	NA|104aa|up_4|NZ_LR699570.1_3082366_3082678_+	NA	NA|203aa|up_3|NZ_LR699570.1_3083097_3083706_+	NA	NA|470aa|up_2|NZ_LR699570.1_3083776_3085186_+	pfam00665, rve, Integrase core domain	NA|271aa|up_1|NZ_LR699570.1_3085182_3085995_+	COG3267, ExeA, Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]	NA|421aa|up_0|NZ_LR699570.1_3087452_3088714_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cas2|114aa|down_0|NZ_LR699570.1_3090967_3091309_-	COG1343, COG1343, CRISPR-associated protein Cas2 [Defense mechanisms]	NA|421aa|down_1|NZ_LR699570.1_3092046_3093308_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	csm5gr7|376aa|down_2|NZ_LR699570.1_3094940_3096068_-	COG1332, COG1332, CRISPR system related protein, RAMP superfamily [Defense mechanisms]	csm4gr5|303aa|down_3|NZ_LR699570.1_3096064_3096973_-	COG1567, COG1567, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	csm3gr7|237aa|down_4|NZ_LR699570.1_3096953_3097664_-	cd09684, Csm3_III-A, CRISPR/Cas system-associated RAMP superfamily protein Csm3	csm2gr11|125aa|down_5|NZ_LR699570.1_3097673_3098048_-	TIGR01870, CRISPR_type_III-associated_protein_Csm2, CRISPR type III-A/MTUBE-associated protein Csm2	cas10|813aa|down_6|NZ_LR699570.1_3098044_3100483_-	cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10	cas6|241aa|down_7|NZ_LR699570.1_3100479_3101202_-	COG5551, COG5551, CRISPR system related protein, RAMP superfamily [Defense    mechanisms]	NA|182aa|down_8|NZ_LR699570.1_3101601_3102147_-	COG4293, COG4293, Uncharacterized protein conserved in bacteria [Function unknown]	NA|295aa|down_9|NZ_LR699570.1_3102418_3103303_-	COG2253, COG2253, Uncharacterized conserved protein [Function unknown]
GCF_902459825.1_MB3601_COMBINED	NZ_LR699570	Mycobacterium tuberculosis variant bovis strain Mb3601 isolate 14Z005608 chromosome Mb3601	9	4063625-4063713	6	CRISPRCasFinder	no		RT,csa3,c2c9_V-U4,cas3,DinG,WYL,cas4,DEDDh,cas2,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,csm5gr7,csm4gr5,csm3gr7,csm2gr11,cas10,cas6	NA|257aa|up_6|NZ_LR699570.1_4054211_4054982_-,NA|233aa|up_0|NZ_LR699570.1_4062729_4063428_-,NA|126aa|down_6|NZ_LR699570.1_4068948_4069326_+	NA|388aa|up_9|NZ_LR699570.1_4049881_4051045_-	TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase	NA|351aa|up_8|NZ_LR699570.1_4051041_4052094_-	TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood CpaE-like protein	NA|288aa|up_7|NZ_LR699570.1_4052593_4053457_+	TIGR01490, Uncharacterized_protein_Rv3661/MT3761, HAD-superfamily subfamily IB hydrolase, TIGR01490	NA|257aa|up_6|NZ_LR699570.1_4054211_4054982_-	NA	NA|549aa|up_5|NZ_LR699570.1_4054978_4056625_-	COG1123, COG1123, ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]	NA|288aa|up_4|NZ_LR699570.1_4056621_4057485_-	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_LR699570.1_4057477_4058404_-	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_LR699570.1_4058405_4060031_-	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_LR699570.1_4060738_4062694_+	PRK00174, PRK00174, acetyl-CoA synthetase; Provisional	NA|233aa|up_0|NZ_LR699570.1_4062729_4063428_-	NA	NA|173aa|down_0|NZ_LR699570.1_4063773_4064292_+	pfam07332, Phage_holin_3_6, Putative Actinobacterial Holin-X, holin superfamily III	NA|328aa|down_1|NZ_LR699570.1_4064292_4065276_+	COG0596, MhpC, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only]	NA|398aa|down_2|NZ_LR699570.1_4065268_4066462_-	pfam13365, Trypsin_2, Trypsin-like peptidase domain	NA|274aa|down_3|NZ_LR699570.1_4066467_4067289_-	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_LR699570.1_4067420_4068104_-	cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA, ResA, DsbE and similar proteins	NA|246aa|down_5|NZ_LR699570.1_4068103_4068841_-	COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]	NA|126aa|down_6|NZ_LR699570.1_4068948_4069326_+	NA	NA|225aa|down_7|NZ_LR699570.1_4069424_4070099_+	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]	NA|265aa|down_8|NZ_LR699570.1_4070204_4070999_-	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_LR699570.1_4071005_4071461_-	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
