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_008727275.1_ASM872727v1	NZ_CP044158	Shigella flexneri strain AR-0423 chromosome, complete genome	1	320758-320873	1	CRISPRCasFinder	no		DEDDh,DinG,RT,PrimPol,cas3,c2c9_V-U4,csa3,TnsE_C	Orphan	GATAAGACGCGCCAGCGTCGCATCAGGCGTT	31	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,RT,PrimPol,cas3,c2c9_V-U4,csa3,TnsE_C	NA,NA	NA|281aa|up_9|NZ_CP044158.1_305914_306757_-	TIGR00668, Bis5'-nucleosyl-tetraphosphatase_symmetrical, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)	NA|126aa|up_8|NZ_CP044158.1_306763_307141_-	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed	NA|274aa|up_7|NZ_CP044158.1_307143_307965_-	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|330aa|up_6|NZ_CP044158.1_307961_308951_-	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|429aa|up_5|NZ_CP044158.1_308950_310237_-	PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional	NA|785aa|up_4|NZ_CP044158.1_310289_312644_-	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional	NA|272aa|up_3|NZ_CP044158.1_312898_313714_+	PRK09430, djlA, co-chaperone DjlA	NA|969aa|up_2|NZ_CP044158.1_314500_317407_-	PRK04914, PRK04914, RNA polymerase-associated protein RapA	NA|784aa|up_1|NZ_CP044158.1_317571_319923_-	PRK05762, PRK05762, DNA polymerase II; Reviewed	NA|232aa|up_0|NZ_CP044158.1_319997_320693_-	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase AraD	NA|501aa|down_0|NZ_CP044158.1_320892_322395_-	PRK02929, PRK02929, L-arabinose isomerase; Provisional	NA|565aa|down_1|NZ_CP044158.1_322405_324100_-	PRK04123, PRK04123, ribulokinase; Provisional	NA|293aa|down_2|NZ_CP044158.1_324438_325317_+	PRK10572, PRK10572, arabinose operon transcriptional regulator AraC	NA|255aa|down_3|NZ_CP044158.1_325402_326167_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|233aa|down_4|NZ_CP044158.1_326280_326979_-	PRK10771, thiQ, thiamine ABC transporter ATP-binding protein ThiQ	NA|537aa|down_5|NZ_CP044158.1_326962_328573_-	PRK09433, thiP, thiamine transporter membrane protein; Reviewed	NA|328aa|down_6|NZ_CP044158.1_328548_329532_-	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional	NA|552aa|down_7|NZ_CP044158.1_329695_331351_-	PRK13626, PRK13626, HTH-type transcriptional regulator SgrR	NA|44aa|down_8|NZ_CP044158.1_331439_331571_+	pfam15894, SgrT, Inhibitor of glucose uptake transporter SgrT	NA|393aa|down_9|NZ_CP044158.1_331672_332851_+	TIGR00899, Sugar_efflux_transporter_A, sugar efflux transporter
GCF_008727275.1_ASM872727v1	NZ_CP044158	Shigella flexneri strain AR-0423 chromosome, complete genome	2	1129154-1129302	2	CRISPRCasFinder	no		DEDDh,DinG,RT,PrimPol,cas3,c2c9_V-U4,csa3,TnsE_C	Orphan	GTTCACTGCCGTACAGGCAGCTTAGAAAT	29	0	0	NA	NA	I-F	2	2	Orphan	DEDDh,DinG,RT,PrimPol,cas3,c2c9_V-U4,csa3,TnsE_C	NA,NA	NA|300aa|up_9|NZ_CP044158.1_1115286_1116186_-	COG2431, COG2431, Predicted membrane protein [Function unknown]	NA|410aa|up_8|NZ_CP044158.1_1116309_1117538_-	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|232aa|up_7|NZ_CP044158.1_1117978_1118674_-	PRK05420, PRK05420, aquaporin Z; Provisional	NA|553aa|up_6|NZ_CP044158.1_1119874_1121533_+	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]	NA|319aa|up_5|NZ_CP044158.1_1121529_1122486_-	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown]	NA|372aa|up_4|NZ_CP044158.1_1122636_1123752_+	PRK11578, PRK11578, macrolide transporter subunit MacA; Provisional	NA|649aa|up_3|NZ_CP044158.1_1123748_1125695_+	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|75aa|up_2|NZ_CP044158.1_1125767_1125992_-	PRK09937, PRK09937, cold shock-like protein CspD	NA|107aa|up_1|NZ_CP044158.1_1126314_1126635_+	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|759aa|up_0|NZ_CP044158.1_1126665_1128942_+	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|73aa|down_0|NZ_CP044158.1_1129685_1129904_-	PRK00276, infA, translation initiation factor IF-1; Validated	NA|235aa|down_1|NZ_CP044158.1_1130188_1130893_-	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|574aa|down_2|NZ_CP044158.1_1130934_1132656_-	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|589aa|down_3|NZ_CP044158.1_1132656_1134423_-	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|322aa|down_4|NZ_CP044158.1_1134545_1135511_-	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|165aa|down_5|NZ_CP044158.1_1136054_1136549_+	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|1343aa|down_6|NZ_CP044158.1_1136683_1140712_+	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|204aa|down_7|NZ_CP044158.1_1140866_1141478_+	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|448aa|down_8|NZ_CP044158.1_1141488_1142832_+	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|431aa|down_9|NZ_CP044158.1_1142922_1144215_+	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional
GCF_008727275.1_ASM872727v1	NZ_CP044158	Shigella flexneri strain AR-0423 chromosome, complete genome	3	2650324-2650450	3	CRISPRCasFinder	no		DEDDh,DinG,RT,PrimPol,cas3,c2c9_V-U4,csa3,TnsE_C	Orphan	TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC	39	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,RT,PrimPol,cas3,c2c9_V-U4,csa3,TnsE_C	NA,NA	NA|550aa|up_9|NZ_CP044158.1_2628703_2630353_-	COG5445, COG5445, Predicted secreted protein [Function unknown]	NA|53aa|up_8|NZ_CP044158.1_2630916_2631075_-	COG2373, COG2373, Large extracellular alpha-helical protein [General function prediction only]	NA|390aa|up_7|NZ_CP044158.1_2632627_2633796_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|208aa|up_6|NZ_CP044158.1_2636144_2636768_-	COG3234, COG3234, Uncharacterized protein conserved in bacteria [Function unknown]	NA|876aa|up_5|NZ_CP044158.1_2638601_2641229_-	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|241aa|up_4|NZ_CP044158.1_2641375_2642098_+	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|645aa|up_3|NZ_CP044158.1_2642225_2644160_-	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|552aa|up_2|NZ_CP044158.1_2644169_2645825_-	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|425aa|up_1|NZ_CP044158.1_2645843_2647117_+	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|762aa|up_0|NZ_CP044158.1_2647987_2650273_+	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|377aa|down_0|NZ_CP044158.1_2650506_2651637_+	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|85aa|down_1|NZ_CP044158.1_2651636_2651891_+	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|217aa|down_2|NZ_CP044158.1_2651944_2652595_-	PRK09902, PRK09902, lipopolysaccharide kinase InaA	NA|359aa|down_3|NZ_CP044158.1_2653057_2654134_-	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|453aa|down_4|NZ_CP044158.1_2654138_2655497_-	PRK11273, glpT, glycerol-3-phosphate transporter	NA|543aa|down_5|NZ_CP044158.1_2655769_2657398_+	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|420aa|down_6|NZ_CP044158.1_2657387_2658647_+	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_7|NZ_CP044158.1_2658643_2659834_+	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|317aa|down_8|NZ_CP044158.1_2660026_2660977_+	PRK09956, PRK09956, ISNCY family transposase	NA|157aa|down_9|NZ_CP044158.1_2661017_2661488_-	PRK10128, PRK10128, 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional
GCF_008727275.1_ASM872727v1	NZ_CP044158	Shigella flexneri strain AR-0423 chromosome, complete genome	4	3120255-3120401	4	CRISPRCasFinder	no		DEDDh,DinG,RT,PrimPol,cas3,c2c9_V-U4,csa3,TnsE_C	Orphan	CTGCTTAAAAAAAGAACAAATGGTAGTGTCCGCTATTGCCAGTACACCTCAAA	53	1	43	3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348|3120308-3120348	NZ_CP044158.1_113616-113656|NZ_CP044158.1_572922-572962|NZ_CP044158.1_955114-955154|NZ_CP044158.1_1080445-1080485|NZ_CP044158.1_1330170-1330210|NZ_CP044158.1_1374467-1374507|NZ_CP044158.1_1398478-1398518|NZ_CP044158.1_1599615-1599655|NZ_CP044158.1_1695094-1695134|NZ_CP044158.1_1714692-1714732|NZ_CP044158.1_1726668-1726708|NZ_CP044158.1_1767255-1767295|NZ_CP044158.1_1775681-1775721|NZ_CP044158.1_1876957-1876997|NZ_CP044158.1_2137341-2137381|NZ_CP044158.1_2188938-2188978|NZ_CP044158.1_2243314-2243354|NZ_CP044158.1_2267253-2267293|NZ_CP044158.1_2373693-2373733|NZ_CP044158.1_2502520-2502560|NZ_CP044158.1_2902174-2902214|NZ_CP044158.1_3345656-3345696|NZ_CP044158.1_4133480-4133520|NZ_CP044158.1_4188874-4188914|NZ_CP044158.1_182202-182162|NZ_CP044158.1_519349-519309|NZ_CP044158.1_567677-567637|NZ_CP044158.1_581388-581348|NZ_CP044158.1_586218-586178|NZ_CP044158.1_967756-967716|NZ_CP044158.1_1166320-1166280|NZ_CP044158.1_1180684-1180644|NZ_CP044158.1_1683225-1683185|NZ_CP044158.1_2128868-2128828|NZ_CP044158.1_2358728-2358688|NZ_CP044158.1_2384808-2384768|NZ_CP044158.1_2394387-2394347|NZ_CP044158.1_979217-979257|NZ_CP044158.1_2980480-2980520|NZ_CP044160.1_19028-18988|NZ_CP044160.1_103502-103462|NZ_CP044160.1_132632-132592|NZ_CP044160.1_142231-142191	NA	1	1	Orphan	DEDDh,DinG,RT,PrimPol,cas3,c2c9_V-U4,csa3,TnsE_C	NA|65aa|up_3|NZ_CP044158.1_3112139_3112334_-,NA	NA|291aa|up_9|NZ_CP044158.1_3105540_3106413_+	PRK10463, PRK10463, hydrogenase nickel incorporation protein HypB; Provisional	NA|91aa|up_8|NZ_CP044158.1_3106403_3106676_+	PRK10409, PRK10409, HypC/HybG/HupF family hydrogenase formation chaperone	NA|374aa|up_7|NZ_CP044158.1_3106675_3107797_+	PRK15062, PRK15062, hydrogenase isoenzymes formation protein HypD; Provisional	NA|337aa|up_6|NZ_CP044158.1_3107793_3108804_+	TIGR02124, Hydrogenase_expression/formation_protein_HypE, hydrogenase expression/formation protein HypE	NA|693aa|up_5|NZ_CP044158.1_3108877_3110956_+	PRK15429, PRK15429, formate hydrogenlyase transcriptional activator FlhA	NA|118aa|up_4|NZ_CP044158.1_3110992_3111346_-	pfam11756, YgbA_NO, Nitrous oxide-stimulated promoter	NA|65aa|up_3|NZ_CP044158.1_3112139_3112334_-	NA	NA|854aa|up_2|NZ_CP044158.1_3112409_3114971_+	PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional	NA|256aa|up_1|NZ_CP044158.1_3115779_3116547_-	COG1349, GlpR, Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]	NA|371aa|up_0|NZ_CP044158.1_3117932_3119044_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|699aa|down_0|NZ_CP044158.1_3120495_3122592_-	pfam09299, Mu-transpos_C, Mu transposase, C-terminal	NA|84aa|down_1|NZ_CP044158.1_3122593_3122845_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|188aa|down_2|NZ_CP044158.1_3123009_3123573_+	pfam07022, Phage_CI_repr, Bacteriophage CI repressor helix-turn-helix domain	NA|198aa|down_3|NZ_CP044158.1_3124792_3125386_-	COG0163, UbiX family flavin prenyltransferase [Coenzyme transport and metabolism]	NA|136aa|down_4|NZ_CP044158.1_3125532_3125940_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|331aa|down_5|NZ_CP044158.1_3126059_3127052_-	PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated	NA|380aa|down_6|NZ_CP044158.1_3127114_3128254_-	PRK10871, nlpD, murein hydrolase activator NlpD	NA|209aa|down_7|NZ_CP044158.1_3128393_3129020_-	PRK00312, pcm, protein-L-isoaspartate(D-aspartate) O-methyltransferase	NA|254aa|down_8|NZ_CP044158.1_3129013_3129775_-	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional	NA|350aa|down_9|NZ_CP044158.1_3129755_3130805_-	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed
GCF_008727275.1_ASM872727v1	NZ_CP044158	Shigella flexneri strain AR-0423 chromosome, complete genome	5	3534339-3534440	5	CRISPRCasFinder	no		DEDDh,DinG,RT,PrimPol,cas3,c2c9_V-U4,csa3,TnsE_C	Orphan	TACAAAACACAACAACATCAACAA	24	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,RT,PrimPol,cas3,c2c9_V-U4,csa3,TnsE_C	NA|55aa|up_0|NZ_CP044158.1_3534133_3534298_+,NA	NA|128aa|up_9|NZ_CP044158.1_3528079_3528463_+	PRK10629, PRK10629, EnvZ/OmpR regulon moderator MzrA	NA|102aa|up_8|NZ_CP044158.1_3529001_3529307_+	COG4575, ElaB, Uncharacterized conserved protein [Function unknown]	NA|135aa|up_7|NZ_CP044158.1_3529309_3529714_+	COG5393, COG5393, Predicted membrane protein [Function unknown]	NA|100aa|up_6|NZ_CP044158.1_3529703_3530003_+	pfam13997, YqjK, YqjK-like protein	NA|129aa|up_5|NZ_CP044158.1_3530098_3530485_+	COG2259, COG2259, Predicted membrane protein [Function unknown]	NA|329aa|up_4|NZ_CP044158.1_3530554_3531541_+	COG0435, ECM4, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]	NA|123aa|up_3|NZ_CP044158.1_3531833_3532202_+	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|299aa|up_2|NZ_CP044158.1_3532408_3533305_-	cd08431, PBP2_HupR, The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold	NA|234aa|up_1|NZ_CP044158.1_3533409_3534111_+	COG1741, COG1741, Pirin-related protein [General function prediction only]	NA|55aa|up_0|NZ_CP044158.1_3534133_3534298_+	NA	NA|444aa|down_0|NZ_CP044158.1_3535846_3537178_-	TIGR00814, membrane_transport_protein_YhjV, serine transporter	NA|455aa|down_1|NZ_CP044158.1_3537452_3538817_-	PRK15040, PRK15040, L-serine ammonia-lyase	NA|130aa|down_2|NZ_CP044158.1_3538888_3539278_-	PRK11401, PRK11401, enamine/imine deaminase	NA|765aa|down_3|NZ_CP044158.1_3539291_3541586_-	cd01678, PFL1, Pyruvate formate lyase 1	NA|403aa|down_4|NZ_CP044158.1_3541619_3542828_-	PRK12379, PRK12379, propionate kinase	NA|444aa|down_5|NZ_CP044158.1_3542853_3544185_-	PRK13629, PRK13629, threonine/serine transporter TdcC; Provisional	NA|330aa|down_6|NZ_CP044158.1_3544206_3545196_-	PRK08638, PRK08638, bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB	NA|313aa|down_7|NZ_CP044158.1_3545294_3546233_-	PRK10341, PRK10341, transcriptional regulator TdcA	NA|115aa|down_8|NZ_CP044158.1_3546422_3546767_+	PRK11424, PRK11424, DNA-binding transcriptional activator TdcR; Provisional	NA|116aa|down_9|NZ_CP044158.1_3547584_3547932_+	PRK09716, PRK09716, YhaC family protein
