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_003719775.1_ASM371977v1	CP033510	Shigella flexneri strain 2016AM-0877 chromosome, complete genome	1	617515-617641	1	CRISPRCasFinder	no		cas3,DEDDh,RT,csa3,DinG,PrimPol,c2c9_V-U4	Orphan	TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC	39	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,RT,csa3,DinG,PrimPol,c2c9_V-U4	NA,NA	NA|259aa|up_9|CP033510.1_595113_595890_-	COG4676, COG4676, Uncharacterized protein conserved in bacteria [Function unknown]	NA|550aa|up_8|CP033510.1_595894_597544_-	COG5445, COG5445, Predicted secreted protein [Function unknown]	NA|390aa|up_7|CP033510.1_599818_600987_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|208aa|up_6|CP033510.1_603335_603959_-	COG3234, COG3234, Uncharacterized protein conserved in bacteria [Function unknown]	NA|876aa|up_5|CP033510.1_605792_608420_-	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|241aa|up_4|CP033510.1_608566_609289_+	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|645aa|up_3|CP033510.1_609416_611351_-	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|552aa|up_2|CP033510.1_611360_613016_-	PRK09752, PRK09752, AIDA-I family autotransporter YfaL	NA|425aa|up_1|CP033510.1_613034_614308_+	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|762aa|up_0|CP033510.1_615178_617464_+	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|377aa|down_0|CP033510.1_617697_618828_+	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|85aa|down_1|CP033510.1_618827_619082_+	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|217aa|down_2|CP033510.1_619135_619786_-	PRK09902, PRK09902, lipopolysaccharide kinase InaA	NA|359aa|down_3|CP033510.1_620248_621325_-	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|453aa|down_4|CP033510.1_621329_622688_-	PRK11273, glpT, glycerol-3-phosphate transporter	NA|543aa|down_5|CP033510.1_622960_624589_+	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|420aa|down_6|CP033510.1_624578_625838_+	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_7|CP033510.1_625834_627025_+	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|317aa|down_8|CP033510.1_627217_628168_+	PRK09956, PRK09956, ISNCY family transposase	NA|157aa|down_9|CP033510.1_628208_628679_-	PRK10128, PRK10128, 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional
GCA_003719775.1_ASM371977v1	CP033510	Shigella flexneri strain 2016AM-0877 chromosome, complete genome	2	1089808-1089954	2	CRISPRCasFinder	no	cas3	cas3,DEDDh,RT,csa3,DinG,PrimPol,c2c9_V-U4	Unclear	CTGCTTAAAAAAAGAACAAATGGTAGTGTCCGCTATTGCCAGTACACCTCAAA	53	1	41	1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901|1089861-1089901	CP033510.1_92900-92860|CP033510.1_101347-101387|CP033510.1_152957-152997|CP033510.1_207333-207373|CP033510.1_231272-231312|CP033510.1_330776-330816|CP033510.1_341891-341851|CP033510.1_351473-351433|CP033510.1_459607-459647|CP033510.1_871725-871765|CP033510.1_1320166-1320206|CP033510.1_2105701-2105741|CP033510.1_2160837-2160877|CP033510.1_2731415-2731455|CP033510.1_2800036-2799996|CP033510.1_3137351-3137311|CP033510.1_3258142-3258102|CP033510.1_3263387-3263427|CP033510.1_3271854-3271814|CP033510.1_3276684-3276644|CP033510.1_3647862-3647902|CP033510.1_3660504-3660464|CP033510.1_3773196-3773236|CP033510.1_3859055-3859015|CP033510.1_4032830-4032790|CP033510.1_4070425-4070465|CP033510.1_4087768-4087808|CP033510.1_4288906-4288946|CP033510.1_4372517-4372477|CP033510.1_4384388-4384428|CP033510.1_4406278-4406318|CP033510.1_4418254-4418294|CP033510.1_4458842-4458882|CP033510.1_4577087-4577127|CP033510.1_950037-950077|CP033510.1_3671965-3672005|CP033511.1_1046-1086|CP033511.1_71853-71813|CP033511.1_110564-110524|CP033511.1_133822-133782|CP033511.1_213391-213351	NA	1	1	Unclear	cas3,DEDDh,RT,csa3,DinG,PrimPol,c2c9_V-U4	NA|65aa|up_3|CP033510.1_1081692_1081887_-,NA	NA|291aa|up_9|CP033510.1_1075093_1075966_+	PRK10463, PRK10463, hydrogenase nickel incorporation protein HypB; Provisional	NA|91aa|up_8|CP033510.1_1075956_1076229_+	PRK10409, PRK10409, HypC/HybG/HupF family hydrogenase formation chaperone	NA|374aa|up_7|CP033510.1_1076228_1077350_+	PRK15062, PRK15062, hydrogenase isoenzymes formation protein HypD; Provisional	NA|337aa|up_6|CP033510.1_1077346_1078357_+	TIGR02124, Hydrogenase_expression/formation_protein_HypE, hydrogenase expression/formation protein HypE	NA|693aa|up_5|CP033510.1_1078430_1080509_+	PRK15429, PRK15429, formate hydrogenlyase transcriptional activator FlhA	NA|118aa|up_4|CP033510.1_1080545_1080899_-	pfam11756, YgbA_NO, Nitrous oxide-stimulated promoter	NA|65aa|up_3|CP033510.1_1081692_1081887_-	NA	NA|854aa|up_2|CP033510.1_1081962_1084524_+	PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional	NA|256aa|up_1|CP033510.1_1085332_1086100_-	COG1349, GlpR, Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]	NA|371aa|up_0|CP033510.1_1087485_1088597_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|699aa|down_0|CP033510.1_1090048_1092145_-	pfam09299, Mu-transpos_C, Mu transposase, C-terminal	NA|84aa|down_1|CP033510.1_1092146_1092398_-	COG3423, Nlp, Predicted transcriptional regulator [Transcription]	NA|188aa|down_2|CP033510.1_1092562_1093126_+	pfam07022, Phage_CI_repr, Bacteriophage CI repressor helix-turn-helix domain	NA|198aa|down_3|CP033510.1_1094345_1094939_-	COG0163, UbiX family flavin prenyltransferase [Coenzyme transport and metabolism]	NA|136aa|down_4|CP033510.1_1095085_1095493_+	smart00347, HTH_MARR, helix_turn_helix multiple antibiotic resistance protein	NA|331aa|down_5|CP033510.1_1095612_1096605_-	PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated	NA|380aa|down_6|CP033510.1_1096667_1097807_-	PRK10871, nlpD, murein hydrolase activator NlpD	NA|209aa|down_7|CP033510.1_1097946_1098573_-	PRK00312, pcm, protein-L-isoaspartate(D-aspartate) O-methyltransferase	NA|254aa|down_8|CP033510.1_1098566_1099328_-	PRK00346, surE, 5'(3')-nucleotidase/polyphosphatase; Provisional	NA|350aa|down_9|CP033510.1_1099308_1100358_-	PRK00984, truD, tRNA pseudouridine synthase D; Reviewed
GCA_003719775.1_ASM371977v1	CP033510	Shigella flexneri strain 2016AM-0877 chromosome, complete genome	3	1508854-1508955	3	CRISPRCasFinder	no		cas3,DEDDh,RT,csa3,DinG,PrimPol,c2c9_V-U4	Orphan	TACAAAACACAACAACATCAACAA	24	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,RT,csa3,DinG,PrimPol,c2c9_V-U4	NA|55aa|up_0|CP033510.1_1508648_1508813_+,NA	NA|128aa|up_9|CP033510.1_1502594_1502978_+	PRK10629, PRK10629, EnvZ/OmpR regulon moderator MzrA	NA|102aa|up_8|CP033510.1_1503516_1503822_+	COG4575, ElaB, Uncharacterized conserved protein [Function unknown]	NA|135aa|up_7|CP033510.1_1503824_1504229_+	COG5393, COG5393, Predicted membrane protein [Function unknown]	NA|100aa|up_6|CP033510.1_1504218_1504518_+	pfam13997, YqjK, YqjK-like protein	NA|129aa|up_5|CP033510.1_1504613_1505000_+	COG2259, COG2259, Predicted membrane protein [Function unknown]	NA|329aa|up_4|CP033510.1_1505069_1506056_+	COG0435, ECM4, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]	NA|123aa|up_3|CP033510.1_1506348_1506717_+	COG3152, COG3152, Predicted membrane protein [Function unknown]	NA|299aa|up_2|CP033510.1_1506923_1507820_-	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|CP033510.1_1507924_1508626_+	COG1741, COG1741, Pirin-related protein [General function prediction only]	NA|55aa|up_0|CP033510.1_1508648_1508813_+	NA	NA|437aa|down_0|CP033510.1_1509024_1510335_-	COG3681, COG3681, L-cysteine desulfidase [Amino acid transport and metabolism]	NA|444aa|down_1|CP033510.1_1510362_1511694_-	TIGR00814, membrane_transport_protein_YhjV, serine transporter	NA|455aa|down_2|CP033510.1_1511968_1513333_-	PRK15040, PRK15040, L-serine ammonia-lyase	NA|130aa|down_3|CP033510.1_1513404_1513794_-	PRK11401, PRK11401, enamine/imine deaminase	NA|765aa|down_4|CP033510.1_1513807_1516102_-	cd01678, PFL1, Pyruvate formate lyase 1	NA|403aa|down_5|CP033510.1_1516135_1517344_-	PRK12379, PRK12379, propionate kinase	NA|444aa|down_6|CP033510.1_1517369_1518701_-	PRK13629, PRK13629, threonine/serine transporter TdcC; Provisional	NA|330aa|down_7|CP033510.1_1518722_1519712_-	PRK08638, PRK08638, bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB	NA|313aa|down_8|CP033510.1_1519810_1520749_-	PRK10341, PRK10341, transcriptional regulator TdcA	NA|115aa|down_9|CP033510.1_1520938_1521283_+	PRK11424, PRK11424, DNA-binding transcriptional activator TdcR; Provisional
GCA_003719775.1_ASM371977v1	CP033510	Shigella flexneri strain 2016AM-0877 chromosome, complete genome	4	2938750-2938865	4	CRISPRCasFinder	no		cas3,DEDDh,RT,csa3,DinG,PrimPol,c2c9_V-U4	Orphan	GATAAGACGCGCCAGCGTCGCATCAGGCGTT	31	0	0	NA	NA	NA	1	1	Orphan	cas3,DEDDh,RT,csa3,DinG,PrimPol,c2c9_V-U4	NA,NA	NA|126aa|up_9|CP033510.1_2924754_2925132_-	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed	NA|274aa|up_8|CP033510.1_2925134_2925956_-	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|330aa|up_7|CP033510.1_2925952_2926942_-	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|429aa|up_6|CP033510.1_2926941_2928228_-	PRK10770, PRK10770, peptidyl-prolyl cis-trans isomerase SurA; Provisional	NA|785aa|up_5|CP033510.1_2928280_2930635_-	PRK03761, PRK03761, LPS assembly outer membrane complex protein LptD; Provisional	NA|272aa|up_4|CP033510.1_2930889_2931705_+	PRK09430, djlA, co-chaperone DjlA	NA|220aa|up_3|CP033510.1_2931821_2932481_-	PRK10158, PRK10158, bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA	NA|969aa|up_2|CP033510.1_2932492_2935399_-	PRK04914, PRK04914, RNA polymerase-associated protein RapA	NA|784aa|up_1|CP033510.1_2935563_2937915_-	PRK05762, PRK05762, DNA polymerase II; Reviewed	NA|232aa|up_0|CP033510.1_2937989_2938685_-	PRK08193, araD, L-ribulose-5-phosphate 4-epimerase AraD	NA|501aa|down_0|CP033510.1_2938884_2940387_-	PRK02929, PRK02929, L-arabinose isomerase; Provisional	NA|567aa|down_1|CP033510.1_2940397_2942098_-	PRK04123, PRK04123, ribulokinase; Provisional	NA|293aa|down_2|CP033510.1_2942436_2943315_+	PRK10572, PRK10572, arabinose operon transcriptional regulator AraC	NA|255aa|down_3|CP033510.1_2943400_2944165_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]	NA|233aa|down_4|CP033510.1_2944278_2944977_-	PRK10771, thiQ, thiamine ABC transporter ATP-binding protein ThiQ	NA|537aa|down_5|CP033510.1_2944960_2946571_-	PRK09433, thiP, thiamine transporter membrane protein; Reviewed	NA|328aa|down_6|CP033510.1_2946546_2947530_-	PRK11205, tbpA, thiamine transporter substrate binding subunit; Provisional	NA|552aa|down_7|CP033510.1_2947693_2949349_-	PRK13626, PRK13626, HTH-type transcriptional regulator SgrR	NA|44aa|down_8|CP033510.1_2949437_2949569_+	pfam15894, SgrT, Inhibitor of glucose uptake transporter SgrT	NA|393aa|down_9|CP033510.1_2949670_2950849_+	TIGR00899, Sugar_efflux_transporter_A, sugar efflux transporter
GCA_003719775.1_ASM371977v1	CP033510	Shigella flexneri strain 2016AM-0877 chromosome, complete genome	5	3821935-3822083	5	CRISPRCasFinder	no		cas3,DEDDh,RT,csa3,DinG,PrimPol,c2c9_V-U4	Orphan	GTTCACTGCCGTACAGGCAGCTTAGAAAT	29	0	0	NA	NA	I-F	2	2	Orphan	cas3,DEDDh,RT,csa3,DinG,PrimPol,c2c9_V-U4	NA,NA	NA|300aa|up_9|CP033510.1_3808067_3808967_-	COG2431, COG2431, Predicted membrane protein [Function unknown]	NA|425aa|up_8|CP033510.1_3809090_3810364_-	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|232aa|up_7|CP033510.1_3810759_3811455_-	PRK05420, PRK05420, aquaporin Z; Provisional	NA|553aa|up_6|CP033510.1_3812655_3814314_+	COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]	NA|331aa|up_5|CP033510.1_3814310_3815303_-	COG2990, VirK, Uncharacterized protein conserved in bacteria [Function unknown]	NA|372aa|up_4|CP033510.1_3815417_3816533_+	PRK11578, PRK11578, macrolide transporter subunit MacA; Provisional	NA|649aa|up_3|CP033510.1_3816529_3818476_+	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|75aa|up_2|CP033510.1_3818548_3818773_-	PRK09937, PRK09937, cold shock-like protein CspD	NA|107aa|up_1|CP033510.1_3819095_3819416_+	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|759aa|up_0|CP033510.1_3819446_3821723_+	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|73aa|down_0|CP033510.1_3822466_3822685_-	PRK00276, infA, translation initiation factor IF-1; Validated	NA|235aa|down_1|CP033510.1_3822969_3823674_-	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|574aa|down_2|CP033510.1_3823715_3825437_-	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|589aa|down_3|CP033510.1_3825437_3827204_-	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|322aa|down_4|CP033510.1_3827326_3828292_-	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|165aa|down_5|CP033510.1_3828835_3829330_+	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|1343aa|down_6|CP033510.1_3829464_3833493_+	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|204aa|down_7|CP033510.1_3833647_3834259_+	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|448aa|down_8|CP033510.1_3834269_3835613_+	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|431aa|down_9|CP033510.1_3835703_3836996_+	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional
