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
GCA_003402955.1_ASM340295v1	CP031546	Escherichia coli strain cq9 chromosome, complete genome	1	664253-664402	1	CRISPRCasFinder	no		DEDDh,cas3,WYL,DinG,c2c9_V-U4,RT,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK	Orphan	CGCGTCTTATCAGGCCTACGAGTTCGGTGCTGTGTAGGTCGGATAAGGCGTTCA	54	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,WYL,DinG,c2c9_V-U4,RT,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK	NA|528aa|up_7|CP031546.1_655459_657043_+,NA|36aa|up_6|CP031546.1_657043_657151_+,NA	NA|198aa|up_9|CP031546.1_654146_654740_+	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|151aa|up_8|CP031546.1_654884_655337_+	COG2731, EbgC, Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]	NA|528aa|up_7|CP031546.1_655459_657043_+	NA	NA|36aa|up_6|CP031546.1_657043_657151_+	NA	NA|338aa|up_5|CP031546.1_657203_658217_-	PRK03515, PRK03515, ornithine carbamoyltransferase subunit I; Provisional	NA|139aa|up_4|CP031546.1_658378_658795_+	PRK11191, PRK11191, ribonuclease E inhibitor RraB	NA|168aa|up_3|CP031546.1_658840_659344_-	pfam00583, Acetyltransf_1, Acetyltransferase (GNAT) family	NA|399aa|up_2|CP031546.1_659536_660733_+	COG4269, COG4269, Predicted membrane protein [Function unknown]	NA|952aa|up_1|CP031546.1_660786_663642_-	PRK05729, valS, valyl-tRNA synthetase; Reviewed	NA|148aa|up_0|CP031546.1_663641_664085_-	PRK05728, PRK05728, DNA polymerase III subunit chi; Validated	NA|504aa|down_0|CP031546.1_664438_665950_-	PRK00913, PRK00913, multifunctional aminopeptidase A; Provisional	NA|367aa|down_1|CP031546.1_666216_667317_+	PRK15120, PRK15120, lipopolysaccharide ABC transporter permease LptF; Provisional	NA|361aa|down_2|CP031546.1_667316_668399_+	PRK15071, PRK15071, lipopolysaccharide ABC transporter permease; Provisional	NA|501aa|down_3|CP031546.1_668559_670062_-	pfam05872, DUF853, Bacterial protein of unknown function (DUF853)	NA|333aa|down_4|CP031546.1_670139_671138_-	cd01575, PBP1_GntR, ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators	NA|440aa|down_5|CP031546.1_671204_672524_-	TIGR00791, Gluconate_permease, gluconate transporter	NA|255aa|down_6|CP031546.1_672586_673351_-	PRK08085, PRK08085, gluconate 5-dehydrogenase; Provisional	NA|344aa|down_7|CP031546.1_673374_674406_-	PRK09880, PRK09880, L-idonate 5-dehydrogenase; Provisional	NA|188aa|down_8|CP031546.1_674622_675186_+	PRK09825, idnK, gluconokinase	NA|340aa|down_9|CP031546.1_675189_676209_-	cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD)
GCA_003402955.1_ASM340295v1	CP031546	Escherichia coli strain cq9 chromosome, complete genome	2	1021009-1021124	2	CRISPRCasFinder	no		DEDDh,cas3,WYL,DinG,c2c9_V-U4,RT,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK	Orphan	GATAAGACGCGCCAGCGTCGCATCAGGCGTT	31	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,WYL,DinG,c2c9_V-U4,RT,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK	NA,NA	NA|126aa|up_9|CP031546.1_1007013_1007391_-	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed	NA|274aa|up_8|CP031546.1_1007393_1008215_-	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|330aa|up_7|CP031546.1_1008211_1009201_-	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|429aa|up_6|CP031546.1_1009200_1010487_-	PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional	NA|785aa|up_5|CP031546.1_1010539_1012894_-	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional	NA|272aa|up_4|CP031546.1_1013148_1013964_+	PRK09430, djlA, co-chaperone DjlA	NA|220aa|up_3|CP031546.1_1014080_1014740_-	PRK10158, PRK10158, bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA	NA|969aa|up_2|CP031546.1_1014751_1017658_-	PRK04914, PRK04914, RNA polymerase-associated protein RapA	NA|784aa|up_1|CP031546.1_1017822_1020174_-	PRK05762, PRK05762, DNA polymerase II; Reviewed	NA|232aa|up_0|CP031546.1_1020248_1020944_-	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase AraD	NA|501aa|down_0|CP031546.1_1021143_1022646_-	PRK02929, PRK02929, L-arabinose isomerase; Provisional	NA|567aa|down_1|CP031546.1_1022656_1024357_-	PRK04123, PRK04123, ribulokinase; Provisional	NA|293aa|down_2|CP031546.1_1024695_1025574_+	PRK10572, PRK10572, arabinose operon transcriptional regulator AraC	NA|255aa|down_3|CP031546.1_1025659_1026424_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|233aa|down_4|CP031546.1_1026537_1027236_-	PRK10771, thiQ, thiamine ABC transporter ATP-binding protein ThiQ	NA|537aa|down_5|CP031546.1_1027219_1028830_-	PRK09433, thiP, thiamine transporter membrane protein; Reviewed	NA|328aa|down_6|CP031546.1_1028805_1029789_-	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional	NA|552aa|down_7|CP031546.1_1029952_1031608_-	PRK13626, PRK13626, HTH-type transcriptional regulator SgrR	NA|44aa|down_8|CP031546.1_1031696_1031828_+	pfam15894, SgrT, Inhibitor of glucose uptake transporter SgrT	NA|393aa|down_9|CP031546.1_1031929_1033108_+	TIGR00899, Sugar_efflux_transporter_A, sugar efflux transporter
GCA_003402955.1_ASM340295v1	CP031546	Escherichia coli strain cq9 chromosome, complete genome	3	1230850-1231003	3	CRISPRCasFinder	no		DEDDh,cas3,WYL,DinG,c2c9_V-U4,RT,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK	Orphan	CGCGTCTTATCATGCCTACAAACCTGTGCCGGATCGGTAGGCCGGATAAGGCG	53	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,WYL,DinG,c2c9_V-U4,RT,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK	NA|150aa|up_8|CP031546.1_1220822_1221272_+,NA|63aa|down_4|CP031546.1_1235274_1235463_-	NA|1418aa|up_9|CP031546.1_1216557_1220811_+	COG3209, RhsA, Rhs family protein [Cell envelope biogenesis, outer membrane]	NA|150aa|up_8|CP031546.1_1220822_1221272_+	NA	NA|257aa|up_7|CP031546.1_1222710_1223481_-	PRK10438, PRK10438, C-N hydrolase family amidase; Provisional	NA|158aa|up_6|CP031546.1_1223634_1224108_+	PRK09993, PRK09993, C-lysozyme inhibitor; Provisional	NA|815aa|up_5|CP031546.1_1224150_1226595_-	PRK09463, fadE, acyl-CoA dehydrogenase; Reviewed	NA|193aa|up_4|CP031546.1_1226834_1227413_+	PRK00414, gmhA, D-sedoheptulose 7-phosphate isomerase	NA|256aa|up_3|CP031546.1_1227618_1228386_+	pfam13230, GATase_4, Glutamine amidotransferases class-II	NA|247aa|up_2|CP031546.1_1228356_1229097_-	COG3034, COG3034, Uncharacterized protein conserved in bacteria [Function unknown]	NA|253aa|up_1|CP031546.1_1229388_1230147_+	COG0791, Spr, Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]	NA|166aa|up_0|CP031546.1_1230322_1230820_+	COG1943, COG1943, Transposase and inactivated derivatives [DNA replication, recombination, and repair]	NA|580aa|down_0|CP031546.1_1231137_1232877_-	COG1298, FlhA, Flagellar biosynthesis pathway, component FlhA [Cell motility and secretion / Intracellular trafficking and secretion]	NA|263aa|down_1|CP031546.1_1232818_1233607_+	PRK06778, PRK06778, hypothetical protein; Validated	NA|352aa|down_2|CP031546.1_1233677_1234733_+	PRK02406, PRK02406, DNA polymerase IV; Validated	NA|151aa|down_3|CP031546.1_1234729_1235182_+	PRK09831, PRK09831, GNAT family N-acetyltransferase	NA|63aa|down_4|CP031546.1_1235274_1235463_-	NA	NA|89aa|down_5|CP031546.1_1235488_1235755_+	PRK09588, PRK09588, hypothetical protein; Reviewed	NA|486aa|down_6|CP031546.1_1236111_1237569_-	PRK15026, PRK15026, aminoacyl-histidine dipeptidase; Provisional	NA|153aa|down_7|CP031546.1_1237829_1238288_+	PRK09177, PRK09177, xanthine-guanine phosphoribosyltransferase; Validated	NA|415aa|down_8|CP031546.1_1238379_1239624_+	PRK05077, frsA, esterase FrsA	NA|134aa|down_9|CP031546.1_1239681_1240083_+	PRK10984, PRK10984, sigma factor-binding protein Crl
GCA_003402955.1_ASM340295v1	CP031546	Escherichia coli strain cq9 chromosome, complete genome	4	4018587-4018981	4,1,1	CRISPRCasFinder,CRT,PILER-CR	no		DEDDh,cas3,WYL,DinG,c2c9_V-U4,RT,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK	Orphan	CGGTTTATCCCCGCTGGCGCGGGGAACTC,CGGTTTATCCCCGCTGGCGCGGGGAACTC,GGTTTATCCCCGCTGGCGCGGGGAACTC	29,29,28	0	0	NA	NA	I-E:I-E:I-E	6,6,6	6	Orphan	DEDDh,cas3,WYL,DinG,c2c9_V-U4,RT,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK	NA,NA|47aa|down_1|CP031546.1_4020130_4020271_+	NA|424aa|up_9|CP031546.1_4007231_4008503_+	PRK10015, PRK10015, oxidoreductase; Provisional	NA|87aa|up_8|CP031546.1_4008493_4008754_+	COG2440, FixX, Ferredoxin-like protein [Energy production and conversion]	NA|192aa|up_7|CP031546.1_4008770_4009346_+	COG1954, GlpP, Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]	NA|287aa|up_6|CP031546.1_4009493_4010354_-	COG2025, FixB, Electron transfer flavoprotein, alpha subunit [Energy production and conversion]	NA|260aa|up_5|CP031546.1_4010350_4011130_-	COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion]	NA|446aa|up_4|CP031546.1_4011107_4012445_-	cd17371, MFS_MucK, Cis,cis-muconate transport protein and similar proteins of the Major Facilitator Superfamily	NA|485aa|up_3|CP031546.1_4012538_4013993_-	COG0277, GlcD, FAD/FMN-containing dehydrogenases [Energy production and conversion]	NA|262aa|up_2|CP031546.1_4014062_4014848_-	cd05347, Ga5DH-like_SDR_c, gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs	NA|426aa|up_1|CP031546.1_4015166_4016444_+	cd06174, MFS, Major Facilitator Superfamily	NA|493aa|up_0|CP031546.1_4016470_4017949_+	cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins	NA|224aa|down_0|CP031546.1_4019320_4019992_-	TIGR04322, organic_radical_activating_enzyme, putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE	NA|47aa|down_1|CP031546.1_4020130_4020271_+	NA	NA|291aa|down_2|CP031546.1_4020284_4021157_+	COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase type [General function prediction only]	NA|433aa|down_3|CP031546.1_4021216_4022515_-	PRK00077, eno, enolase; Provisional	NA|546aa|down_4|CP031546.1_4022602_4024240_-	PRK05380, pyrG, CTP synthetase; Validated	NA|264aa|down_5|CP031546.1_4024467_4025259_-	PRK09562, mazG, nucleoside triphosphate pyrophosphohydrolase; Reviewed	NA|112aa|down_6|CP031546.1_4025329_4025665_-	PRK09907, PRK09907, endoribonuclease MazF	NA|83aa|down_7|CP031546.1_4025664_4025913_-	PRK09798, PRK09798, MazF-MazE toxin-antitoxin system antitoxin MazE	NA|745aa|down_8|CP031546.1_4025990_4028225_-	PRK10872, relA, (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional	NA|434aa|down_9|CP031546.1_4028272_4029574_-	PRK13168, rumA, 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
GCA_003402955.1_ASM340295v1	CP031546	Escherichia coli strain cq9 chromosome, complete genome	5	4543829-4543968	5	CRISPRCasFinder	no		DEDDh,cas3,WYL,DinG,c2c9_V-U4,RT,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK	Orphan	TGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAACGACACAAA	49	0	0	NA	NA	NA	1	1	Orphan	DEDDh,cas3,WYL,DinG,c2c9_V-U4,RT,csa3,cas2,cas1,cas6e,cas5,cas7,cse2gr11,cas8e,PD-DExK	NA,NA	NA|252aa|up_9|CP031546.1_4533099_4533855_+	PRK09762, PRK09762, galactosamine-6-phosphate isomerase; Provisional	NA|195aa|up_8|CP031546.1_4534255_4534840_+	COG3539, FimA, P pilus assembly protein, pilin FimA [Cell motility and secretion / Intracellular trafficking and secretion]	NA|232aa|up_7|CP031546.1_4534919_4535615_+	COG3121, FimC, P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]	NA|839aa|up_6|CP031546.1_4535644_4538161_+	COG3188, FimD, P pilus assembly protein, porin PapC [Cell motility and secretion / Intracellular trafficking and secretion]	NA|364aa|up_5|CP031546.1_4538171_4539263_+	pfam00419, Fimbrial, Fimbrial protein	NA|287aa|up_4|CP031546.1_4539305_4540166_-	PRK14994, PRK14994, SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional	NA|679aa|up_3|CP031546.1_4540230_4542267_+	COG3107, LppC, Putative lipoprotein [General function prediction only]	NA|132aa|up_2|CP031546.1_4542224_4542620_+	TIGR00252, UPF0102_protein_HI_1656, TIGR00252 family protein	NA|197aa|up_1|CP031546.1_4542639_4543230_+	PRK10886, PRK10886, DnaA initiator-associating protein DiaA; Provisional	NA|192aa|up_0|CP031546.1_4543239_4543815_+	PRK11023, PRK11023, divisome-associated lipoprotein YraP	NA|347aa|down_0|CP031546.1_4544019_4545060_-	COG0701, COG0701, Predicted permeases [General function prediction only]	NA|212aa|down_1|CP031546.1_4545132_4545768_-	cd05250, CC3_like_SDR_a, CC3(TIP30)-like, atypical (a) SDRs	NA|173aa|down_2|CP031546.1_4545895_4546414_+	cd03134, GATase1_PfpI_like, A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus	NA|148aa|down_3|CP031546.1_4546393_4546837_-	PRK03467, PRK03467, hypothetical protein; Provisional	NA|101aa|down_4|CP031546.1_4546887_4547190_+	PRK00329, PRK00329, GIY-YIG nuclease superfamily protein; Validated	NA|168aa|down_5|CP031546.1_4547176_4547680_-	COG3153, COG3153, Predicted acetyltransferase [General function prediction only]	NA|175aa|down_6|CP031546.1_4547673_4548198_-	COG3154, COG3154, Putative lipid carrier protein [Lipid metabolism]	NA|332aa|down_7|CP031546.1_4548406_4549402_+	COG0826, COG0826, Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]	NA|293aa|down_8|CP031546.1_4549410_4550289_+	PRK15447, PRK15447, putative protease; Provisional	NA|336aa|down_9|CP031546.1_4550494_4551502_+	PRK10508, PRK10508, luciferase-like monooxygenase
