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_001612475.1_ASM161247v1	NZ_CP015020	Escherichia coli strain 28RC1 chromosome, complete genome	1	28076-28225	1	CRISPRCasFinder	no	DEDDh	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	Unclear	TACCAGAGATAGCGAACCGTAGGTCGGAAAAGGCGCTCGCGCCGCATCCGACA	53	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	NA|22aa|up_2|NZ_CP015020.1_26163_26229_+,NA	NA|83aa|up_9|NZ_CP015020.1_20379_20628_-	PRK10597, PRK10597, DNA damage-inducible protein I; Provisional	NA|189aa|up_8|NZ_CP015020.1_20945_21512_-	PRK11440, PRK11440, putative hydrolase; Provisional	NA|591aa|up_7|NZ_CP015020.1_21821_23594_+	PRK00476, aspS, aspartyl-tRNA synthetase; Validated	NA|151aa|up_6|NZ_CP015020.1_23711_24164_+	PRK09438, nudB, dihydroneopterin triphosphate pyrophosphatase; Provisional	NA|247aa|up_5|NZ_CP015020.1_24192_24933_+	PRK00110, PRK00110, YebC/PmpR family DNA-binding transcriptional regulator	NA|174aa|up_4|NZ_CP015020.1_24967_25489_+	TIGR00228, Crossover_junction_endodeoxyribonuclease_RuvC, crossover junction endodeoxyribonuclease RuvC	NA|201aa|up_3|NZ_CP015020.1_25490_26093_-	PRK11470, PRK11470, YebB family permuted papain-like enzyme	NA|22aa|up_2|NZ_CP015020.1_26163_26229_+	NA	NA|204aa|up_1|NZ_CP015020.1_26367_26979_+	PRK00116, ruvA, Holliday junction branch migration protein RuvA	NA|337aa|up_0|NZ_CP015020.1_26987_27998_+	PRK00080, ruvB, Holliday junction branch migration DNA helicase RuvB	NA|262aa|down_0|NZ_CP015020.1_28243_29029_-	PRK09543, znuB, zinc ABC transporter permease subunit ZnuB	NA|252aa|down_1|NZ_CP015020.1_29025_29781_-	PRK09544, znuC, high-affinity zinc transporter ATPase; Reviewed	NA|311aa|down_2|NZ_CP015020.1_29859_30792_+	PRK09545, znuA, zinc ABC transporter substrate-binding protein ZnuA	NA|441aa|down_3|NZ_CP015020.1_30807_32130_+	PRK11649, PRK11649, putative peptidase; Provisional	NA|324aa|down_4|NZ_CP015020.1_32249_33221_+	PRK08943, PRK08943, lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase; Validated	NA|481aa|down_5|NZ_CP015020.1_33351_34794_-	PRK05826, PRK05826, pyruvate kinase; Provisional	NA|290aa|down_6|NZ_CP015020.1_34921_35791_-	PRK11302, PRK11302, DNA-binding transcriptional regulator HexR; Provisional	NA|492aa|down_7|NZ_CP015020.1_36128_37604_+	PRK05722, PRK05722, glucose-6-phosphate 1-dehydrogenase; Validated	NA|604aa|down_8|NZ_CP015020.1_37838_39650_+	PRK09054, PRK09054, phosphogluconate dehydratase; Validated	NA|214aa|down_9|NZ_CP015020.1_39686_40328_+	PRK05718, PRK05718, keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
GCF_001612475.1_ASM161247v1	NZ_CP015020	Escherichia coli strain 28RC1 chromosome, complete genome	2	226678-226801	2	CRISPRCasFinder	no	DEDDh	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	Unclear	CGACCCCCACCATGTCAAGGTGGTGCTCTAACCAACTGAGCTA	43	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	NA,NA|30aa|down_7|NZ_CP015020.1_235697_235787_+	NA|471aa|up_9|NZ_CP015020.1_216131_217544_-	PRK09206, PRK09206, pyruvate kinase PykF	NA|70aa|up_8|NZ_CP015020.1_218100_218310_+	PRK10292, PRK10292, fumarate hydratase FumD	NA|209aa|up_7|NZ_CP015020.1_218765_219392_+	PRK09898, PRK09898, ferredoxin-like protein	NA|701aa|up_6|NZ_CP015020.1_219412_221515_+	PRK09849, PRK09849, putative oxidoreductase; Provisional	NA|213aa|up_5|NZ_CP015020.1_221527_222166_+	PRK09947, PRK09947, YdhW family putative oxidoreductase system protein	NA|223aa|up_4|NZ_CP015020.1_222229_222898_+	TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S protein	NA|262aa|up_3|NZ_CP015020.1_222894_223680_+	PRK15006, PRK15006, thiosulfate reductase cytochrome B subunit; Provisional	NA|271aa|up_2|NZ_CP015020.1_223683_224496_+	PRK09946, PRK09946, hypothetical protein; Provisional	NA|535aa|up_1|NZ_CP015020.1_224507_226112_-	PRK09897, PRK09897, FAD-NAD(P)-binding protein	NA|102aa|up_0|NZ_CP015020.1_226237_226543_-	PRK11118, PRK11118, putative monooxygenase; Provisional	NA|419aa|down_0|NZ_CP015020.1_227115_228372_+	PRK09945, PRK09945, hypothetical protein; Provisional	NA|458aa|down_1|NZ_CP015020.1_228412_229786_-	PRK01766, PRK01766, multidrug efflux protein; Reviewed	NA|214aa|down_2|NZ_CP015020.1_230000_230642_+	PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional	NA|383aa|down_3|NZ_CP015020.1_230681_231830_-	PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase	NA|404aa|down_4|NZ_CP015020.1_232120_233332_-	PRK11043, PRK11043, Bcr/CflA family multidrug efflux MFS transporter	NA|311aa|down_5|NZ_CP015020.1_233444_234377_+	PRK11074, PRK11074, putative DNA-binding transcriptional regulator; Provisional	NA|342aa|down_6|NZ_CP015020.1_234373_235399_-	PRK10703, PRK10703, HTH-type transcriptional repressor PurR	NA|30aa|down_7|NZ_CP015020.1_235697_235787_+	NA	NA|390aa|down_8|NZ_CP015020.1_235952_237122_+	COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]	NA|194aa|down_9|NZ_CP015020.1_237267_237849_-	PRK10543, PRK10543, superoxide dismutase [Fe]
GCF_001612475.1_ASM161247v1	NZ_CP015020	Escherichia coli strain 28RC1 chromosome, complete genome	3	1886868-1887080	3,1,1	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,cas3	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	Type I-E	CGGTTTATCCCCGCTGGCGCGGGGAACAC,CGGTTTATCCCCGCTGGCGCGGGGAACACA,CGGTTTATCCCCGCTGGCGCGGGGAACACA	29,30,30	0	0	NA	NA	I-E:I-E:I-E	3,3,2	3	TypeI-E	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	NA,NA	NA|254aa|up_9|NZ_CP015020.1_1878680_1879442_-	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional	NA|350aa|up_8|NZ_CP015020.1_1879422_1880472_-	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|160aa|up_7|NZ_CP015020.1_1880468_1880948_-	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|237aa|up_6|NZ_CP015020.1_1880947_1881658_-	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|104aa|up_5|NZ_CP015020.1_1881676_1881988_-	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|108aa|up_4|NZ_CP015020.1_1882181_1882505_-	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|202aa|up_3|NZ_CP015020.1_1882554_1883160_-	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|476aa|up_2|NZ_CP015020.1_1883159_1884587_-	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|303aa|up_1|NZ_CP015020.1_1884588_1885497_-	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|346aa|up_0|NZ_CP015020.1_1885748_1886786_+	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	cas2|98aa|down_0|NZ_CP015020.1_1887175_1887469_-	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	cas1|308aa|down_1|NZ_CP015020.1_1887465_1888389_-	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas6e|217aa|down_2|NZ_CP015020.1_1888385_1889036_-	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas5|249aa|down_3|NZ_CP015020.1_1889017_1889764_-	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas7|352aa|down_4|NZ_CP015020.1_1889774_1890830_-	TIGR01869, CRISPR_system_Cascade_subunit_CasC, CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI	cse2gr11|179aa|down_5|NZ_CP015020.1_1890841_1891378_-	TIGR02548, CRISPR_system_Cascade_subunit_CasB, CRISPR type I-E/ECOLI-associated protein CasB/Cse2	cas8e|521aa|down_6|NZ_CP015020.1_1891374_1892937_-	TIGR02547, CRISPR_system_Cascade_subunit_CasA, CRISPR type I-E/ECOLI-associated protein CasA/Cse1	cas3|900aa|down_7|NZ_CP015020.1_1893034_1895734_-	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	NA|51aa|down_8|NZ_CP015020.1_1895925_1896078_-	pfam01848, HOK_GEF, Hok/gef family	NA|245aa|down_9|NZ_CP015020.1_1896341_1897076_-	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase
GCF_001612475.1_ASM161247v1	NZ_CP015020	Escherichia coli strain 28RC1 chromosome, complete genome	4	1912772-1912860	4	CRISPRCasFinder	no	cas3	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	Unclear	GGTTTATCCCCACTGGCGCGGGGAACTC	28	0	0	NA	NA	I-E	1	1	Unclear	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	NA,NA	NA|600aa|up_9|NZ_CP015020.1_1898861_1900661_-	PRK10953, cysJ, NADPH-dependent assimilatory sulfite reductase flavoprotein subunit	NA|121aa|up_8|NZ_CP015020.1_1900979_1901342_+	cd00470, PTPS, 6-pyruvoyl tetrahydropterin synthase (PTPS)	NA|424aa|up_7|NZ_CP015020.1_1901419_1902691_+	PRK10015, PRK10015, oxidoreductase; Provisional	NA|87aa|up_6|NZ_CP015020.1_1902681_1902942_+	COG2440, FixX, Ferredoxin-like protein [Energy production and conversion]	NA|192aa|up_5|NZ_CP015020.1_1902958_1903534_+	COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]	NA|260aa|up_4|NZ_CP015020.1_1904538_1905318_-	COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion]	NA|485aa|up_3|NZ_CP015020.1_1906725_1908180_-	COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion]	NA|262aa|up_2|NZ_CP015020.1_1908249_1909035_-	cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs	NA|426aa|up_1|NZ_CP015020.1_1909353_1910631_+	cd06174, MFS, Major Facilitator Superfamily	NA|493aa|up_0|NZ_CP015020.1_1910657_1912136_+	cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins	NA|224aa|down_0|NZ_CP015020.1_1913199_1913871_-	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|207aa|down_1|NZ_CP015020.1_1914025_1914646_+	COG1704, LemA, Uncharacterized conserved protein [Function unknown]	NA|225aa|down_2|NZ_CP015020.1_1914659_1915334_+	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]	NA|383aa|down_3|NZ_CP015020.1_1915567_1916716_+	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]	NA|305aa|down_4|NZ_CP015020.1_1916712_1917627_+	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]	NA|433aa|down_5|NZ_CP015020.1_1917686_1918985_-	PRK00077, eno, enolase; Provisional	NA|546aa|down_6|NZ_CP015020.1_1919072_1920710_-	PRK05380, pyrG, CTP synthetase; Validated	NA|264aa|down_7|NZ_CP015020.1_1920937_1921729_-	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|112aa|down_8|NZ_CP015020.1_1921799_1922135_-	PRK09907, PRK09907, endoribonuclease MazF	NA|83aa|down_9|NZ_CP015020.1_1922134_1922383_-	PRK09798, PRK09798, MazF-MazE toxin-antitoxin system antitoxin MazE
GCF_001612475.1_ASM161247v1	NZ_CP015020	Escherichia coli strain 28RC1 chromosome, complete genome	5	3601567-3601716	5	CRISPRCasFinder	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	Orphan	CGCGTCTTATCAGGCCTACGAGTTCGGTGCTGTGTAGGTCGGATAAGGCGTTCA	54	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	NA|573aa|up_6|NZ_CP015020.1_3592750_3594469_+,NA	NA|238aa|up_9|NZ_CP015020.1_3590653_3591367_-	PRK12742, PRK12742, SDR family oxidoreductase	NA|198aa|up_8|NZ_CP015020.1_3591437_3592031_+	pfam00440, TetR_N, Bacterial regulatory proteins, tetR family	NA|151aa|up_7|NZ_CP015020.1_3592175_3592628_+	COG2731, EbgC, Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]	NA|573aa|up_6|NZ_CP015020.1_3592750_3594469_+	NA	NA|335aa|up_5|NZ_CP015020.1_3594525_3595530_-	PRK03515, PRK03515, ornithine carbamoyltransferase subunit I; Provisional	NA|139aa|up_4|NZ_CP015020.1_3595691_3596108_+	PRK11191, PRK11191, ribonuclease E inhibitor RraB	NA|168aa|up_3|NZ_CP015020.1_3596153_3596657_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|399aa|up_2|NZ_CP015020.1_3596849_3598046_+	COG4269, COG4269, Predicted membrane protein [Function unknown]	NA|952aa|up_1|NZ_CP015020.1_3598100_3600956_-	PRK05729, valS, valyl-tRNA synthetase; Reviewed	NA|148aa|up_0|NZ_CP015020.1_3600955_3601399_-	PRK05728, PRK05728, DNA polymerase III subunit chi; Validated	NA|504aa|down_0|NZ_CP015020.1_3601752_3603264_-	PRK00913, PRK00913, multifunctional aminopeptidase A; Provisional	NA|367aa|down_1|NZ_CP015020.1_3603530_3604631_+	PRK15120, PRK15120, lipopolysaccharide ABC transporter permease LptF; Provisional	NA|361aa|down_2|NZ_CP015020.1_3604630_3605713_+	PRK15071, PRK15071, lipopolysaccharide ABC transporter permease; Provisional	NA|501aa|down_3|NZ_CP015020.1_3605873_3607376_-	pfam05872, DUF853, Bacterial protein of unknown function (DUF853)	NA|340aa|down_4|NZ_CP015020.1_3607505_3608525_-	cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD)	NA|650aa|down_5|NZ_CP015020.1_3608895_3610845_+	cd01184, INT_C_like_1, Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain	NA|405aa|down_6|NZ_CP015020.1_3611044_3612258_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|126aa|down_7|NZ_CP015020.1_3612440_3612818_-	pfam13711, DUF4160, Domain of unknown function (DUF4160)	NA|111aa|down_8|NZ_CP015020.1_3612939_3613272_-	pfam07978, NIPSNAP, NIPSNAP	NA|156aa|down_9|NZ_CP015020.1_3614275_3614743_-	COG4333, COG4333, Uncharacterized protein conserved in bacteria [Function unknown]
GCF_001612475.1_ASM161247v1	NZ_CP015020	Escherichia coli strain 28RC1 chromosome, complete genome	6	3834084-3834218	6	CRISPRCasFinder	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	Orphan	TGCCGGATGCGCGTTGCTTATCCGGCCTACAAAATCGCAGCGTGTAGGCC	50	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK,PrimPol	NA|251aa|up_4|NZ_CP015020.1_3826037_3826790_+,NA|190aa|down_7|NZ_CP015020.1_3843259_3843829_+	NA|274aa|up_9|NZ_CP015020.1_3819172_3819994_-	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|330aa|up_8|NZ_CP015020.1_3819990_3820980_-	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|429aa|up_7|NZ_CP015020.1_3820979_3822266_-	PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional	NA|785aa|up_6|NZ_CP015020.1_3822318_3824673_-	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional	NA|272aa|up_5|NZ_CP015020.1_3824927_3825743_+	PRK09430, djlA, co-chaperone DjlA	NA|251aa|up_4|NZ_CP015020.1_3826037_3826790_+	NA	NA|220aa|up_3|NZ_CP015020.1_3827207_3827867_-	PRK10158, PRK10158, bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA	NA|969aa|up_2|NZ_CP015020.1_3827878_3830785_-	PRK04914, PRK04914, RNA polymerase-associated protein RapA	NA|784aa|up_1|NZ_CP015020.1_3830948_3833300_-	PRK05762, PRK05762, DNA polymerase II; Reviewed	NA|232aa|up_0|NZ_CP015020.1_3833374_3834070_-	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase AraD	NA|501aa|down_0|NZ_CP015020.1_3834269_3835772_-	PRK02929, PRK02929, L-arabinose isomerase; Provisional	NA|567aa|down_1|NZ_CP015020.1_3835782_3837483_-	PRK04123, PRK04123, ribulokinase; Provisional	NA|293aa|down_2|NZ_CP015020.1_3837821_3838700_+	PRK10572, PRK10572, arabinose operon transcriptional regulator AraC	NA|255aa|down_3|NZ_CP015020.1_3838785_3839550_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|233aa|down_4|NZ_CP015020.1_3839636_3840335_-	PRK10771, thiQ, thiamine ABC transporter ATP-binding protein ThiQ	NA|537aa|down_5|NZ_CP015020.1_3840318_3841929_-	PRK09433, thiP, thiamine transporter membrane protein; Reviewed	NA|328aa|down_6|NZ_CP015020.1_3841904_3842888_-	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional	NA|190aa|down_7|NZ_CP015020.1_3843259_3843829_+	NA	NA|553aa|down_8|NZ_CP015020.1_3844057_3845716_-	PRK13626, PRK13626, HTH-type transcriptional regulator SgrR	NA|44aa|down_9|NZ_CP015020.1_3845804_3845936_+	pfam15894, SgrT, Inhibitor of glucose uptake transporter SgrT
