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_003019135.1_ASM301913v1	NZ_CP027464	Escherichia coli strain 2013C-4248 chromosome, complete genome	1	821013-821529	1,1,1	PILER-CR,CRISPRCasFinder,CRT	no	cas3	cas3,cse2gr11,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,c2c9_V-U4,WYL,PrimPol,PD-DExK	Unclear	GAGTTCCCCGCGCCAGCGGGGATAAACCG,GAGTTCCCCGCGCCAGCGGGGATAAACCG,GAGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	8,8,8	8	Unclear	cas3,cse2gr11,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,c2c9_V-U4,WYL,PrimPol,PD-DExK,TnsE_C	NA|47aa|up_1|NZ_CP027464.1_819722_819863_-,NA	NA|919aa|up_9|NZ_CP027464.1_807606_810363_-	PRK11107, PRK11107, hybrid sensory histidine kinase BarA; Provisional	NA|434aa|up_8|NZ_CP027464.1_810419_811721_+	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD	NA|745aa|up_7|NZ_CP027464.1_811768_814003_+	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|83aa|up_6|NZ_CP027464.1_814080_814329_+	PRK09798, PRK09798, MazF-MazE toxin-antitoxin system antitoxin MazE	NA|112aa|up_5|NZ_CP027464.1_814328_814664_+	PRK09907, PRK09907, endoribonuclease MazF	NA|264aa|up_4|NZ_CP027464.1_814734_815526_+	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|546aa|up_3|NZ_CP027464.1_815753_817391_+	PRK05380, pyrG, CTP synthetase; Validated	NA|433aa|up_2|NZ_CP027464.1_817478_818777_+	PRK00077, eno, enolase; Provisional	NA|47aa|up_1|NZ_CP027464.1_819722_819863_-	NA	NA|224aa|up_0|NZ_CP027464.1_820001_820673_+	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|493aa|down_0|NZ_CP027464.1_822168_823647_-	cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins	NA|426aa|down_1|NZ_CP027464.1_823673_824951_-	cd06174, MFS, Major Facilitator Superfamily	NA|262aa|down_2|NZ_CP027464.1_825268_826054_+	cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs	NA|485aa|down_3|NZ_CP027464.1_826123_827578_+	COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion]	NA|446aa|down_4|NZ_CP027464.1_827671_829009_+	cd17371, MFS_MucK, Cis,cis-muconate transport protein and similar proteins of the Major Facilitator Superfamily	NA|260aa|down_5|NZ_CP027464.1_828986_829766_+	COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion]	NA|287aa|down_6|NZ_CP027464.1_829762_830623_+	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|192aa|down_7|NZ_CP027464.1_830770_831346_-	COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]	NA|87aa|down_8|NZ_CP027464.1_831362_831623_-	COG2440, FixX, Ferredoxin-like protein [Energy production and conversion]	NA|424aa|down_9|NZ_CP027464.1_831613_832885_-	PRK10015, PRK10015, oxidoreductase; Provisional
GCF_003019135.1_ASM301913v1	NZ_CP027464	Escherichia coli strain 2013C-4248 chromosome, complete genome	2	848560-848954	2,2,2	PILER-CR,CRISPRCasFinder,CRT	no	cas3,cse2gr11,cas5,cas6e,cas1,cas2	cas3,cse2gr11,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,c2c9_V-U4,WYL,PrimPol,PD-DExK	Type I-E	GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG,GTGTTCCCCGCGCCAGCGGGGATAAACCG	29,29,29	0	0	NA	NA	I-E:I-E:I-E	6,6,6	6	TypeI-E	cas3,cse2gr11,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,c2c9_V-U4,WYL,PrimPol,PD-DExK,TnsE_C	NA,NA	NA|571aa|up_9|NZ_CP027464.1_835442_837155_+	PRK13504, PRK13504, NADPH-dependent assimilatory sulfite reductase hemoprotein subunit	NA|245aa|up_8|NZ_CP027464.1_837228_837963_+	PRK02090, PRK02090, phosphoadenylyl-sulfate reductase	NA|51aa|up_7|NZ_CP027464.1_838227_838380_+	pfam01848, HOK_GEF, Hok/gef family	cas3|900aa|up_6|NZ_CP027464.1_838573_841273_+	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	NA|405aa|up_5|NZ_CP027464.1_841607_842821_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	cse2gr11|178aa|up_4|NZ_CP027464.1_844242_844776_+	TIGR02548, CRISPR_system_Cascade_subunit_CasB, CRISPR type I-E/ECOLI-associated protein CasB/Cse2	cas5|249aa|up_3|NZ_CP027464.1_845874_846621_+	cd09645, Cas5_I-E, CRISPR/Cas system-associated RAMP superfamily protein Cas5	cas6e|217aa|up_2|NZ_CP027464.1_846602_847253_+	TIGR01907, CRISPR_system_Cascade_subunit_CasE, CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI	cas1|307aa|up_1|NZ_CP027464.1_847249_848170_+	TIGR03638, cas1_ECOLI, CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI	cas2|98aa|up_0|NZ_CP027464.1_848169_848463_+	PRK11558, PRK11558, putative ssRNA endonuclease; Provisional	NA|346aa|down_0|NZ_CP027464.1_849035_850073_-	PRK10199, PRK10199, alkaline phosphatase isozyme conversion aminopeptidase; Provisional	NA|303aa|down_1|NZ_CP027464.1_850324_851233_+	PRK05253, PRK05253, sulfate adenylyltransferase subunit CysD	NA|476aa|down_2|NZ_CP027464.1_851234_852662_+	PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional	NA|202aa|down_3|NZ_CP027464.1_852661_853267_+	PRK03846, PRK03846, adenylylsulfate kinase; Provisional	NA|108aa|down_4|NZ_CP027464.1_853316_853640_+	pfam12084, DUF3561, Protein of unknown function (DUF3561)	NA|104aa|down_5|NZ_CP027464.1_853833_854145_+	PRK00888, ftsB, cell division protein FtsB; Reviewed	NA|237aa|down_6|NZ_CP027464.1_854163_854874_+	PRK00155, ispD, D-ribitol-5-phosphate cytidylyltransferase	NA|160aa|down_7|NZ_CP027464.1_854873_855353_+	PRK00084, ispF, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed	NA|350aa|down_8|NZ_CP027464.1_855349_856399_+	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed	NA|254aa|down_9|NZ_CP027464.1_856379_857141_+	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional
GCF_003019135.1_ASM301913v1	NZ_CP027464	Escherichia coli strain 2013C-4248 chromosome, complete genome	3	2183278-2183401	3	CRISPRCasFinder	no	DEDDh	cas3,cse2gr11,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,c2c9_V-U4,WYL,PrimPol,PD-DExK	Unclear	CGACCCCCACCATGTCAAGGTGGTGCTCTAACCAACTGAGCTA	43	0	0	NA	NA	NA	1	1	Orphan	cas3,cse2gr11,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,c2c9_V-U4,WYL,PrimPol,PD-DExK,TnsE_C	NA,NA|75aa|down_7|NZ_CP027464.1_2191986_2192211_-,NA|30aa|down_8|NZ_CP027464.1_2192297_2192387_+	NA|70aa|up_9|NZ_CP027464.1_2173387_2173597_+	PRK10292, PRK10292, fumarate hydratase FumD	NA|209aa|up_8|NZ_CP027464.1_2174052_2174679_+	PRK09898, PRK09898, ferredoxin-like protein	NA|405aa|up_7|NZ_CP027464.1_2175660_2176874_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|387aa|up_6|NZ_CP027464.1_2176954_2178115_+	PRK09849, PRK09849, putative oxidoreductase; Provisional	NA|216aa|up_5|NZ_CP027464.1_2178118_2178766_+	PRK09947, PRK09947, YdhW family putative oxidoreductase system protein	NA|223aa|up_4|NZ_CP027464.1_2178829_2179498_+	TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S protein	NA|262aa|up_3|NZ_CP027464.1_2179494_2180280_+	PRK15006, PRK15006, thiosulfate reductase cytochrome B subunit; Provisional	NA|271aa|up_2|NZ_CP027464.1_2180283_2181096_+	PRK09946, PRK09946, hypothetical protein; Provisional	NA|535aa|up_1|NZ_CP027464.1_2181107_2182712_-	PRK09897, PRK09897, FAD-NAD(P)-binding protein	NA|102aa|up_0|NZ_CP027464.1_2182837_2183143_-	PRK11118, PRK11118, putative monooxygenase; Provisional	NA|419aa|down_0|NZ_CP027464.1_2183715_2184972_+	PRK09945, PRK09945, hypothetical protein; Provisional	NA|458aa|down_1|NZ_CP027464.1_2185012_2186386_-	PRK01766, PRK01766, multidrug efflux protein; Reviewed	NA|214aa|down_2|NZ_CP027464.1_2186600_2187242_+	PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional	NA|383aa|down_3|NZ_CP027464.1_2187281_2188430_-	PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase	NA|404aa|down_4|NZ_CP027464.1_2188720_2189932_-	PRK11043, PRK11043, Bcr/CflA family multidrug efflux MFS transporter	NA|311aa|down_5|NZ_CP027464.1_2190044_2190977_+	PRK11074, PRK11074, putative DNA-binding transcriptional regulator; Provisional	NA|342aa|down_6|NZ_CP027464.1_2190973_2191999_-	PRK10703, PRK10703, HTH-type transcriptional repressor PurR	NA|75aa|down_7|NZ_CP027464.1_2191986_2192211_-	NA	NA|30aa|down_8|NZ_CP027464.1_2192297_2192387_+	NA	NA|390aa|down_9|NZ_CP027464.1_2192552_2193722_+	COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]
GCF_003019135.1_ASM301913v1	NZ_CP027464	Escherichia coli strain 2013C-4248 chromosome, complete genome	4	3893131-3893246	4	CRISPRCasFinder	no		cas3,cse2gr11,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,c2c9_V-U4,WYL,PrimPol,PD-DExK	Orphan	AACGCCTGATGCGACGCTGACGCGTCTTATC	31	0	0	NA	NA	NA	1	1	Orphan	cas3,cse2gr11,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,c2c9_V-U4,WYL,PrimPol,PD-DExK,TnsE_C	NA,NA	NA|393aa|up_9|NZ_CP027464.1_3881146_3882325_-	TIGR00899, Sugar_efflux_transporter_A, sugar efflux transporter	NA|44aa|up_8|NZ_CP027464.1_3882426_3882558_-	pfam15894, SgrT, Inhibitor of glucose uptake transporter SgrT	NA|552aa|up_7|NZ_CP027464.1_3882646_3884302_+	PRK13626, PRK13626, HTH-type transcriptional regulator SgrR	NA|328aa|up_6|NZ_CP027464.1_3884465_3885449_+	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional	NA|537aa|up_5|NZ_CP027464.1_3885424_3887035_+	PRK09433, thiP, thiamine transporter membrane protein; Reviewed	NA|233aa|up_4|NZ_CP027464.1_3887018_3887717_+	PRK10771, thiQ, thiamine ABC transporter ATP-binding protein ThiQ	NA|255aa|up_3|NZ_CP027464.1_3887830_3888595_-	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|293aa|up_2|NZ_CP027464.1_3888680_3889559_-	PRK10572, PRK10572, arabinose operon transcriptional regulator AraC	NA|567aa|up_1|NZ_CP027464.1_3889897_3891598_+	PRK04123, PRK04123, ribulokinase; Provisional	NA|501aa|up_0|NZ_CP027464.1_3891608_3893111_+	PRK02929, PRK02929, L-arabinose isomerase; Provisional	NA|232aa|down_0|NZ_CP027464.1_3893311_3894007_+	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase AraD	NA|784aa|down_1|NZ_CP027464.1_3894081_3896433_+	PRK05762, PRK05762, DNA polymerase II; Reviewed	NA|969aa|down_2|NZ_CP027464.1_3896597_3899504_+	PRK04914, PRK04914, RNA polymerase-associated protein RapA	NA|220aa|down_3|NZ_CP027464.1_3899515_3900175_+	PRK10158, PRK10158, bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA	NA|272aa|down_4|NZ_CP027464.1_3900291_3901107_-	PRK09430, djlA, co-chaperone DjlA	NA|785aa|down_5|NZ_CP027464.1_3901361_3903716_+	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional	NA|429aa|down_6|NZ_CP027464.1_3903768_3905055_+	PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional	NA|330aa|down_7|NZ_CP027464.1_3905054_3906044_+	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|274aa|down_8|NZ_CP027464.1_3906040_3906862_+	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|126aa|down_9|NZ_CP027464.1_3906864_3907242_+	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed
GCF_003019135.1_ASM301913v1	NZ_CP027468	Escherichia coli strain 2013C-4248 plasmid unnamed4	1	18271-18378	1	PILER-CR	no		c2c9_V-U4	Orphan	ACAGTCAACATAAAATCGCGTACAGTCAATGTT	33	1	1	18347-18359	NZ_CP027469.1_32960-32972	NA	2	2	Orphan	cas3,cse2gr11,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,c2c9_V-U4,WYL,PrimPol,PD-DExK,TnsE_C	NA|82aa|up_9|NZ_CP027468.1_7085_7331_+,NA|199aa|up_8|NZ_CP027468.1_7513_8110_-,NA|170aa|up_7|NZ_CP027468.1_8281_8791_-,NA|194aa|up_6|NZ_CP027468.1_8802_9384_-,NA|272aa|up_5|NZ_CP027468.1_9419_10235_-,NA|530aa|up_4|NZ_CP027468.1_10244_11834_-,NA|569aa|up_3|NZ_CP027468.1_11894_13601_-,NA|295aa|up_0|NZ_CP027468.1_17310_18195_-,NA|131aa|down_0|NZ_CP027468.1_18528_18921_-,NA|141aa|down_1|NZ_CP027468.1_19098_19521_-,NA|263aa|down_2|NZ_CP027468.1_19560_20349_-,NA|95aa|down_4|NZ_CP027468.1_20811_21096_+,NA|64aa|down_7|NZ_CP027468.1_26548_26740_-,NA|79aa|down_8|NZ_CP027468.1_26935_27172_+	NA|82aa|up_9|NZ_CP027468.1_7085_7331_+	NA	NA|199aa|up_8|NZ_CP027468.1_7513_8110_-	NA	NA|170aa|up_7|NZ_CP027468.1_8281_8791_-	NA	NA|194aa|up_6|NZ_CP027468.1_8802_9384_-	NA	NA|272aa|up_5|NZ_CP027468.1_9419_10235_-	NA	NA|530aa|up_4|NZ_CP027468.1_10244_11834_-	NA	NA|569aa|up_3|NZ_CP027468.1_11894_13601_-	NA	NA|334aa|up_2|NZ_CP027468.1_13825_14827_-	pfam08775, ParB, ParB family	NA|399aa|up_1|NZ_CP027468.1_14843_16040_-	pfam18607, HTH_54, ParA helix turn helix domain	NA|295aa|up_0|NZ_CP027468.1_17310_18195_-	NA	NA|131aa|down_0|NZ_CP027468.1_18528_18921_-	NA	NA|141aa|down_1|NZ_CP027468.1_19098_19521_-	NA	NA|263aa|down_2|NZ_CP027468.1_19560_20349_-	NA	NA|60aa|down_3|NZ_CP027468.1_20357_20537_-	cd14737, PAAR_1, proline-alanine-alanine-arginine (PAAR) domain	NA|95aa|down_4|NZ_CP027468.1_20811_21096_+	NA	NA|302aa|down_5|NZ_CP027468.1_21088_21994_+	PRK00321, rdgC, recombination associated protein; Reviewed	NA|1096aa|down_6|NZ_CP027468.1_21990_25278_+	TIGR00571, DNA_adenine_methylase, DNA adenine methylase (dam)	NA|64aa|down_7|NZ_CP027468.1_26548_26740_-	NA	NA|79aa|down_8|NZ_CP027468.1_26935_27172_+	NA	NA|276aa|down_9|NZ_CP027468.1_27152_27980_+	pfam01145, Band_7, SPFH domain / Band 7 family
GCF_003019135.1_ASM301913v1	NZ_CP027465	Escherichia coli strain 2013C-4248 plasmid unnamed1, complete sequence	1	25173-25264	1	CRISPRCasFinder	no	TnsE_C	TnsE_C,csa3	Orphan	TGAAAAAGTGAAAAAATTTCACTTT	25	0	0	NA	NA	NA	1	1	Orphan	cas3,cse2gr11,cas5,cas6e,cas1,cas2,csa3,DEDDh,DinG,c2c9_V-U4,WYL,PrimPol,PD-DExK,TnsE_C	NA|199aa|up_8|NZ_CP027465.1_20062_20659_+,NA|72aa|up_6|NZ_CP027465.1_22140_22356_+,NA|145aa|up_5|NZ_CP027465.1_22352_22787_+,NA|89aa|up_4|NZ_CP027465.1_22879_23146_+,NA|130aa|up_3|NZ_CP027465.1_23322_23712_+,NA|72aa|down_0|NZ_CP027465.1_25402_25618_+,NA|111aa|down_2|NZ_CP027465.1_27243_27576_+	NA|240aa|up_9|NZ_CP027465.1_19346_20066_+	PRK13704, PRK13704, plasmid SOS inhibition protein A; Provisional	NA|199aa|up_8|NZ_CP027465.1_20062_20659_+	NA	NA|167aa|up_7|NZ_CP027465.1_21120_21621_+	pfam07275, ArdA, Antirestriction protein (ArdA)	NA|72aa|up_6|NZ_CP027465.1_22140_22356_+	NA	NA|145aa|up_5|NZ_CP027465.1_22352_22787_+	NA	NA|89aa|up_4|NZ_CP027465.1_22879_23146_+	NA	NA|130aa|up_3|NZ_CP027465.1_23322_23712_+	NA	NA|309aa|up_2|NZ_CP027465.1_23708_24635_+	PRK09956, PRK09956, ISNCY family transposase	NA|74aa|up_1|NZ_CP027465.1_24658_24880_+	TIGR01784, Uncharacterized_protein_pSLT051, conserved hypothetical protein (putative transposase or invertase)	NA|84aa|up_0|NZ_CP027465.1_24910_25162_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|72aa|down_0|NZ_CP027465.1_25402_25618_+	NA	NA|112aa|down_1|NZ_CP027465.1_26675_27011_-	cd16149, sulfatase_like, uncharacterized sulfatase subfamily	NA|111aa|down_2|NZ_CP027465.1_27243_27576_+	NA	NA|904aa|down_3|NZ_CP027465.1_27587_30299_+	pfam03432, Relaxase, Relaxase/Mobilisation nuclease domain	NA|226aa|down_4|NZ_CP027465.1_30607_31285_+	pfam01527, HTH_Tnp_1, Transposase	NA|116aa|down_5|NZ_CP027465.1_31284_31632_+	pfam05717, TnpB_IS66, IS66 Orf2 like protein	NA|524aa|down_6|NZ_CP027465.1_31651_33223_+	pfam03050, DDE_Tnp_IS66, Transposase IS66 family	NA|80aa|down_7|NZ_CP027465.1_34367_34607_+	pfam08849, DUF1819, Putative inner membrane protein (DUF1819)	NA|109aa|down_8|NZ_CP027465.1_34794_35121_-	TIGR02249, Integrase/recombinase_E2_protein	NA|179aa|down_9|NZ_CP027465.1_35235_35772_-	TIGR02249, Integrase/recombinase_E2_protein
