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_001281425.1_ASM128142v1	NZ_CP010413	Bifidobacterium breve strain BR3, complete genome	1	44471-44617	1	CRISPRCasFinder	no		WYL,cas3,DEDDh,RT,c2c9_V-U4	Orphan	CTTAGCGACAGGATTTTAGGAGATT	25	1	1	44496-44531	NZ_CP010413.1_43159-43194	NA	2	2	Orphan	WYL,cas3,DEDDh,RT,c2c9_V-U4	NA|318aa|up_0|NZ_CP010413.1_43402_44356_-,NA|702aa|down_3|NZ_CP010413.1_47321_49427_-	NA|1021aa|up_9|NZ_CP010413.1_32033_35096_+	TIGR00757, Ribonuclease_E/G-like_protein, ribonuclease, Rne/Rng family	NA|103aa|up_8|NZ_CP010413.1_35282_35591_+	PRK05573, rplU, 50S ribosomal protein L21; Validated	NA|84aa|up_7|NZ_CP010413.1_35613_35865_+	PRK05435, rpmA, 50S ribosomal protein L27; Validated	NA|564aa|up_6|NZ_CP010413.1_35931_37623_+	PRK12296, obgE, GTPase CgtA; Reviewed	NA|378aa|up_5|NZ_CP010413.1_37730_38864_+	PRK05429, PRK05429, gamma-glutamyl kinase; Provisional	NA|421aa|up_4|NZ_CP010413.1_38959_40222_-	cd10966, CE4_yadE_5s, Putative catalytic polysaccharide deacetylase domain of uncharacterized protein yadE and similar proteins	NA|402aa|up_3|NZ_CP010413.1_40363_41569_+	PRK05764, PRK05764, aspartate aminotransferase; Provisional	NA|76aa|up_2|NZ_CP010413.1_41898_42126_+	PRK07597, secE, preprotein translocase subunit SecE; Reviewed	NA|276aa|up_1|NZ_CP010413.1_42158_42986_+	PRK05609, nusG, transcription antitermination protein NusG; Validated	NA|318aa|up_0|NZ_CP010413.1_43402_44356_-	NA	NA|144aa|down_0|NZ_CP010413.1_44972_45404_+	PRK00140, rplK, 50S ribosomal protein L11; Validated	NA|231aa|down_1|NZ_CP010413.1_45419_46112_+	PRK05424, rplA, 50S ribosomal protein L1; Validated	NA|286aa|down_2|NZ_CP010413.1_46385_47243_-	COG2508, COG2508, Regulator of polyketide synthase expression [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]	NA|702aa|down_3|NZ_CP010413.1_47321_49427_-	NA	NA|320aa|down_4|NZ_CP010413.1_49598_50558_+	COG0340, BirA, Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme metabolism]	NA|181aa|down_5|NZ_CP010413.1_50559_51102_-	pfam02632, BioY, BioY family	NA|623aa|down_6|NZ_CP010413.1_51671_53540_+	COG4770, COG4770, Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism]	NA|541aa|down_7|NZ_CP010413.1_53532_55155_+	COG4799, COG4799, Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta) [Lipid metabolism]	NA|3161aa|down_8|NZ_CP010413.1_55194_64677_+	COG4982, COG4982, 3-oxoacyl-[acyl-carrier protein]	NA|75aa|down_9|NZ_CP010413.1_66075_66300_+	cd17489, MFS_YfcJ_like, Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily
GCF_001281425.1_ASM128142v1	NZ_CP010413	Bifidobacterium breve strain BR3, complete genome	2	430395-430837	1,1,2	PILER-CR,CRT,CRISPRCasFinder	no		WYL,cas3,DEDDh,RT,c2c9_V-U4	Orphan	GTCGCTCCCCATCCGGGGAGCGTGGATTGAAAT,GTCGCTCCCCATCCGGGGAGCGTGGATTGAAAT,TCCCCATCCGGGGAGCGTGGATTGAAAT	33,33,28	0	0	NA	NA	I-C:I-C:I-C	5,6,6	6	Orphan	WYL,cas3,DEDDh,RT,c2c9_V-U4	NA,NA	NA|758aa|up_9|NZ_CP010413.1_413401_415675_+	PRK15098, PRK15098, beta-glucosidase BglX	NA|178aa|up_8|NZ_CP010413.1_415885_416419_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|654aa|up_7|NZ_CP010413.1_416415_418377_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|672aa|up_6|NZ_CP010413.1_418373_420389_+	COG1132, MdlB, ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]	NA|342aa|up_5|NZ_CP010413.1_420567_421593_+	cd06299, PBP1_LacI-like, ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum produces significant amounts of L-glutamate directly from cheap sugar and ammonia	NA|321aa|up_4|NZ_CP010413.1_421812_422775_+	cd02650, nuc_hydro_CaPnhB, NH_hydro_CaPnhB: A subgroup of nucleoside hydrolases similar to Corynebacterium ammoniagenes Purine/pyrimidine nucleoside hydrolase (pnhB)	NA|467aa|up_3|NZ_CP010413.1_422803_424204_+	cd17325, MFS_MdtG_SLC18_like, bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily of transporters	NA|322aa|up_2|NZ_CP010413.1_424291_425257_+	cd01174, ribokinase, Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP	NA|1103aa|up_1|NZ_CP010413.1_425928_429237_+	PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed	NA|205aa|up_0|NZ_CP010413.1_429655_430270_+	pfam13542, HTH_Tnp_ISL3, Helix-turn-helix domain of transposase family ISL3	NA|407aa|down_0|NZ_CP010413.1_431872_433093_-	PRK05250, PRK05250, S-adenosylmethionine synthetase; Validated	NA|95aa|down_1|NZ_CP010413.1_433378_433663_-	PRK00392, rpoZ, DNA-directed RNA polymerase subunit omega; Reviewed	NA|621aa|down_2|NZ_CP010413.1_433830_435693_+	PRK12448, PRK12448, dihydroxy-acid dehydratase; Provisional	NA|338aa|down_3|NZ_CP010413.1_435989_437003_-	PRK00005, fmt, methionyl-tRNA formyltransferase; Reviewed	NA|235aa|down_4|NZ_CP010413.1_437141_437846_-	cd02603, HAD_sEH-N_like, N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX/HAD4 alpha-D-glucose 1-phosphate phosphatase, and related domains, may be inactive	NA|770aa|down_5|NZ_CP010413.1_437995_440305_-	PRK14873, PRK14873, primosomal protein N'	NA|251aa|down_6|NZ_CP010413.1_440352_441105_-	cd07500, HAD_PSP, phosphoserine phosphatase (PSP), similar to Methanococcus Jannaschii PSP and Saccharomyces cerevisiae SER2p	NA|232aa|down_7|NZ_CP010413.1_441125_441821_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|525aa|down_8|NZ_CP010413.1_441874_443449_+	TIGR03689, pup_AAA, proteasome ATPase	NA|238aa|down_9|NZ_CP010413.1_443508_444222_-	cd02603, HAD_sEH-N_like, N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX/HAD4 alpha-D-glucose 1-phosphate phosphatase, and related domains, may be inactive
GCF_001281425.1_ASM128142v1	NZ_CP010413	Bifidobacterium breve strain BR3, complete genome	3	1827101-1827272	2	PILER-CR	no	RT	WYL,cas3,DEDDh,RT,c2c9_V-U4	Unclear	CCAGACGCTCGTCCATACGCCGCTGATGGCGTTCAGGACG	40	0	0	NA	NA	NA	2	2	Orphan	WYL,cas3,DEDDh,RT,c2c9_V-U4	NA|95aa|up_8|NZ_CP010413.1_1814567_1814852_+,NA|108aa|up_5|NZ_CP010413.1_1816562_1816886_-,NA|527aa|up_3|NZ_CP010413.1_1818823_1820404_-,NA|199aa|up_2|NZ_CP010413.1_1821295_1821892_-,NA|260aa|up_0|NZ_CP010413.1_1825641_1826421_-,NA|107aa|down_1|NZ_CP010413.1_1829914_1830235_-,NA|196aa|down_2|NZ_CP010413.1_1830289_1830877_-,NA|122aa|down_3|NZ_CP010413.1_1830908_1831274_-,NA|92aa|down_4|NZ_CP010413.1_1831270_1831546_-,NA|112aa|down_5|NZ_CP010413.1_1831557_1831893_-,NA|105aa|down_7|NZ_CP010413.1_1832353_1832668_-,NA|178aa|down_9|NZ_CP010413.1_1833618_1834152_-	NA|91aa|up_9|NZ_CP010413.1_1814311_1814584_+	pfam04365, BrnT_toxin, Ribonuclease toxin, BrnT, of type II toxin-antitoxin system	NA|95aa|up_8|NZ_CP010413.1_1814567_1814852_+	NA	NA|88aa|up_7|NZ_CP010413.1_1814917_1815181_-	pfam16938, Phage_holin_Dp1, Putative phage holin Dp-1	NA|412aa|up_6|NZ_CP010413.1_1815265_1816501_-	cd06417, GH25_LysA-like, LysA is a cell wall endolysin produced by Lactobacillus fermentum, which degrades bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues	NA|108aa|up_5|NZ_CP010413.1_1816562_1816886_-	NA	RT|412aa|up_4|NZ_CP010413.1_1817174_1818410_-	cd01651, RT_G2_intron, RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin	NA|527aa|up_3|NZ_CP010413.1_1818823_1820404_-	NA	NA|199aa|up_2|NZ_CP010413.1_1821295_1821892_-	NA	NA|1240aa|up_1|NZ_CP010413.1_1821901_1825621_-	pfam06605, Prophage_tail, Prophage endopeptidase tail	NA|260aa|up_0|NZ_CP010413.1_1825641_1826421_-	NA	NA|131aa|down_0|NZ_CP010413.1_1829510_1829903_-	pfam17318, DUF5361, Family of unknown function (DUF5361)	NA|107aa|down_1|NZ_CP010413.1_1829914_1830235_-	NA	NA|196aa|down_2|NZ_CP010413.1_1830289_1830877_-	NA	NA|122aa|down_3|NZ_CP010413.1_1830908_1831274_-	NA	NA|92aa|down_4|NZ_CP010413.1_1831270_1831546_-	NA	NA|112aa|down_5|NZ_CP010413.1_1831557_1831893_-	NA	NA|151aa|down_6|NZ_CP010413.1_1831889_1832342_-	pfam09355, Phage_Gp19, Phage protein Gp19/Gp15/Gp42	NA|105aa|down_7|NZ_CP010413.1_1832353_1832668_-	NA	NA|302aa|down_8|NZ_CP010413.1_1832667_1833573_-	pfam05065, Phage_capsid, Phage capsid family	NA|178aa|down_9|NZ_CP010413.1_1833618_1834152_-	NA
GCF_001281425.1_ASM128142v1	NZ_CP010413	Bifidobacterium breve strain BR3, complete genome	4	1834182-1834261	3	CRISPRCasFinder	no	RT	WYL,cas3,DEDDh,RT,c2c9_V-U4	Unclear	CGGGCATTGAAAAAGCCACCCGTGCG	26	0	0	NA	NA	NA	1	1	Orphan	WYL,cas3,DEDDh,RT,c2c9_V-U4	NA|107aa|up_8|NZ_CP010413.1_1829914_1830235_-,NA|196aa|up_7|NZ_CP010413.1_1830289_1830877_-,NA|122aa|up_6|NZ_CP010413.1_1830908_1831274_-,NA|92aa|up_5|NZ_CP010413.1_1831270_1831546_-,NA|112aa|up_4|NZ_CP010413.1_1831557_1831893_-,NA|105aa|up_2|NZ_CP010413.1_1832353_1832668_-,NA|178aa|up_0|NZ_CP010413.1_1833618_1834152_-,NA|87aa|down_0|NZ_CP010413.1_1834283_1834544_-,NA|401aa|down_1|NZ_CP010413.1_1834501_1835704_-,NA|63aa|down_4|NZ_CP010413.1_1838570_1838759_-,NA|280aa|down_6|NZ_CP010413.1_1839647_1840487_-,NA|62aa|down_7|NZ_CP010413.1_1840634_1840820_-,NA|152aa|down_8|NZ_CP010413.1_1840816_1841272_-,NA|73aa|down_9|NZ_CP010413.1_1841268_1841487_-	NA|131aa|up_9|NZ_CP010413.1_1829510_1829903_-	pfam17318, DUF5361, Family of unknown function (DUF5361)	NA|107aa|up_8|NZ_CP010413.1_1829914_1830235_-	NA	NA|196aa|up_7|NZ_CP010413.1_1830289_1830877_-	NA	NA|122aa|up_6|NZ_CP010413.1_1830908_1831274_-	NA	NA|92aa|up_5|NZ_CP010413.1_1831270_1831546_-	NA	NA|112aa|up_4|NZ_CP010413.1_1831557_1831893_-	NA	NA|151aa|up_3|NZ_CP010413.1_1831889_1832342_-	pfam09355, Phage_Gp19, Phage protein Gp19/Gp15/Gp42	NA|105aa|up_2|NZ_CP010413.1_1832353_1832668_-	NA	NA|302aa|up_1|NZ_CP010413.1_1832667_1833573_-	pfam05065, Phage_capsid, Phage capsid family	NA|178aa|up_0|NZ_CP010413.1_1833618_1834152_-	NA	NA|87aa|down_0|NZ_CP010413.1_1834283_1834544_-	NA	NA|401aa|down_1|NZ_CP010413.1_1834501_1835704_-	NA	NA|500aa|down_2|NZ_CP010413.1_1835654_1837154_-	pfam05133, Phage_prot_Gp6, Phage portal protein, SPP1 Gp6-like	NA|478aa|down_3|NZ_CP010413.1_1837153_1838587_-	TIGR01547, Uncharacterized_protein_YqaT, phage terminase, large subunit, PBSX family	NA|63aa|down_4|NZ_CP010413.1_1838570_1838759_-	NA	NA|98aa|down_5|NZ_CP010413.1_1838948_1839242_-	pfam14279, HNH_5, HNH endonuclease	NA|280aa|down_6|NZ_CP010413.1_1839647_1840487_-	NA	NA|62aa|down_7|NZ_CP010413.1_1840634_1840820_-	NA	NA|152aa|down_8|NZ_CP010413.1_1840816_1841272_-	NA	NA|73aa|down_9|NZ_CP010413.1_1841268_1841487_-	NA
GCF_001281425.1_ASM128142v1	NZ_CP010413	Bifidobacterium breve strain BR3, complete genome	5	2045205-2045384	4	CRISPRCasFinder	no		WYL,cas3,DEDDh,RT,c2c9_V-U4	Orphan	CCTCAGCGGGGCAAAACCACCAG	23	0	0	NA	NA	NA	3	3	Orphan	WYL,cas3,DEDDh,RT,c2c9_V-U4	NA|262aa|up_3|NZ_CP010413.1_2039394_2040180_+,NA	NA|320aa|up_9|NZ_CP010413.1_2026594_2027554_-	cd05827, Sortase_C, Sortase domain found in class C sortases	NA|615aa|up_8|NZ_CP010413.1_2027810_2029655_-	pfam16569, GramPos_pilinBB, Gram-positive pilin backbone subunit 2, Cna-B-like domain	NA|1471aa|up_7|NZ_CP010413.1_2029759_2034172_-	pfam17802, SpaA, Prealbumin-like fold domain	NA|344aa|up_6|NZ_CP010413.1_2035045_2036077_+	COG1609, PurR, Transcriptional regulators [Transcription]	NA|605aa|up_5|NZ_CP010413.1_2036348_2038163_+	cd11332, AmyAc_OligoGlu_TS, Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), trehalose synthase (also called maltose alpha-D-glucosyltransferase), and related proteins	NA|343aa|up_4|NZ_CP010413.1_2038369_2039398_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|262aa|up_3|NZ_CP010413.1_2039394_2040180_+	NA	NA|351aa|up_2|NZ_CP010413.1_2040482_2041535_-	PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional	NA|351aa|up_1|NZ_CP010413.1_2041962_2043015_-	PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional	NA|456aa|up_0|NZ_CP010413.1_2043410_2044778_-	cd17369, MFS_ShiA_like, Shikimate transporter and similar proteins of the Major Facilitator Superfamily	NA|351aa|down_0|NZ_CP010413.1_2045768_2046821_-	cd06291, PBP1_Qymf-like, ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs	NA|545aa|down_1|NZ_CP010413.1_2046890_2048525_-	cd06174, MFS, Major Facilitator Superfamily	NA|509aa|down_2|NZ_CP010413.1_2048729_2050256_-	PRK13840, PRK13840, sucrose phosphorylase; Provisional	NA|362aa|down_3|NZ_CP010413.1_2050682_2051768_-	cd06291, PBP1_Qymf-like, ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs	NA|132aa|down_4|NZ_CP010413.1_2052042_2052438_-	pfam02537, CRCB, CrcB-like protein, Camphor Resistance (CrcB)	NA|347aa|down_5|NZ_CP010413.1_2052437_2053478_-	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|528aa|down_6|NZ_CP010413.1_2053664_2055248_-	cd01031, EriC, ClC chloride channel EriC	NA|429aa|down_7|NZ_CP010413.1_2055271_2056558_-	PRK01117, PRK01117, adenylosuccinate synthetase; Provisional	NA|356aa|down_8|NZ_CP010413.1_2056711_2057779_-	PRK09197, PRK09197, fructose-bisphosphate aldolase; Provisional	NA|312aa|down_9|NZ_CP010413.1_2057841_2058777_-	TIGR00950, Uncharacterized_inner_membrane_transporter_YicL, Carboxylate/Amino Acid/Amine Transporter
GCF_001281425.1_ASM128142v1	NZ_CP010413	Bifidobacterium breve strain BR3, complete genome	6	2045465-2045539	5	CRISPRCasFinder	no		WYL,cas3,DEDDh,RT,c2c9_V-U4	Orphan	CCTCAGCGGGGCAAAACCACCAG	23	0	0	NA	NA	NA	1	1	Orphan	WYL,cas3,DEDDh,RT,c2c9_V-U4	NA|262aa|up_3|NZ_CP010413.1_2039394_2040180_+,NA	NA|320aa|up_9|NZ_CP010413.1_2026594_2027554_-	cd05827, Sortase_C, Sortase domain found in class C sortases	NA|615aa|up_8|NZ_CP010413.1_2027810_2029655_-	pfam16569, GramPos_pilinBB, Gram-positive pilin backbone subunit 2, Cna-B-like domain	NA|1471aa|up_7|NZ_CP010413.1_2029759_2034172_-	pfam17802, SpaA, Prealbumin-like fold domain	NA|344aa|up_6|NZ_CP010413.1_2035045_2036077_+	COG1609, PurR, Transcriptional regulators [Transcription]	NA|605aa|up_5|NZ_CP010413.1_2036348_2038163_+	cd11332, AmyAc_OligoGlu_TS, Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), trehalose synthase (also called maltose alpha-D-glucosyltransferase), and related proteins	NA|343aa|up_4|NZ_CP010413.1_2038369_2039398_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|262aa|up_3|NZ_CP010413.1_2039394_2040180_+	NA	NA|351aa|up_2|NZ_CP010413.1_2040482_2041535_-	PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional	NA|351aa|up_1|NZ_CP010413.1_2041962_2043015_-	PRK05479, PRK05479, ketol-acid reductoisomerase; Provisional	NA|456aa|up_0|NZ_CP010413.1_2043410_2044778_-	cd17369, MFS_ShiA_like, Shikimate transporter and similar proteins of the Major Facilitator Superfamily	NA|351aa|down_0|NZ_CP010413.1_2045768_2046821_-	cd06291, PBP1_Qymf-like, ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs	NA|545aa|down_1|NZ_CP010413.1_2046890_2048525_-	cd06174, MFS, Major Facilitator Superfamily	NA|509aa|down_2|NZ_CP010413.1_2048729_2050256_-	PRK13840, PRK13840, sucrose phosphorylase; Provisional	NA|362aa|down_3|NZ_CP010413.1_2050682_2051768_-	cd06291, PBP1_Qymf-like, ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs	NA|132aa|down_4|NZ_CP010413.1_2052042_2052438_-	pfam02537, CRCB, CrcB-like protein, Camphor Resistance (CrcB)	NA|347aa|down_5|NZ_CP010413.1_2052437_2053478_-	COG0239, CrcB, Integral membrane protein possibly involved in chromosome condensation [Cell division and chromosome partitioning]	NA|528aa|down_6|NZ_CP010413.1_2053664_2055248_-	cd01031, EriC, ClC chloride channel EriC	NA|429aa|down_7|NZ_CP010413.1_2055271_2056558_-	PRK01117, PRK01117, adenylosuccinate synthetase; Provisional	NA|356aa|down_8|NZ_CP010413.1_2056711_2057779_-	PRK09197, PRK09197, fructose-bisphosphate aldolase; Provisional	NA|312aa|down_9|NZ_CP010413.1_2057841_2058777_-	TIGR00950, Uncharacterized_inner_membrane_transporter_YicL, Carboxylate/Amino Acid/Amine Transporter
