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_003265245.1_ASM326524v1	CP022672	Shigella sonnei strain 866 chromosome, complete genome	1	778876-779005	1	CRISPRCasFinder	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11	Orphan	ATGCTGGCGCATCTTATCCAGCCTACGGTTGCTCTCCAGC	40	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11,TnsE_C	NA,NA	NA|314aa|up_9|CP022672.1_764769_765711_+	PRK05627, PRK05627, bifunctional riboflavin kinase/FAD synthetase	NA|939aa|up_8|CP022672.1_765753_768570_+	PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed	NA|165aa|up_7|CP022672.1_768569_769064_+	PRK00376, lspA, lipoprotein signal peptidase	NA|150aa|up_6|CP022672.1_769188_769638_+	PRK15095, PRK15095, FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional	NA|317aa|up_5|CP022672.1_769639_770590_+	PRK01045, ispH, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed	NA|305aa|up_4|CP022672.1_770655_771570_+	PRK10768, PRK10768, ribonucleoside hydrolase RihC; Provisional	NA|274aa|up_3|CP022672.1_771736_772558_+	COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism]	NA|383aa|up_2|CP022672.1_773013_774162_+	PRK12564, PRK12564, carbamoyl-phosphate synthase small subunit	NA|1074aa|up_1|CP022672.1_774179_777401_+	PRK05294, carB, carbamoyl-phosphate synthase large subunit	NA|132aa|up_0|CP022672.1_778438_778834_+	PRK11476, PRK11476, carnitine metabolism transcriptional regulator CaiF	NA|197aa|down_0|CP022672.1_779042_779633_-	PRK13627, PRK13627, carnitine operon protein CaiE; Provisional	NA|262aa|down_1|CP022672.1_779638_780424_-	PRK03580, PRK03580, crotonobetainyl-CoA hydratase	NA|518aa|down_2|CP022672.1_780532_782086_-	PRK08008, caiC, putative crotonobetaine/carnitine-CoA ligase; Validated	NA|386aa|down_3|CP022672.1_782249_783406_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|381aa|down_4|CP022672.1_784772_785915_-	PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated	NA|505aa|down_5|CP022672.1_785945_787460_-	PRK03356, PRK03356, L-carnitine/gamma-butyrobetaine antiport BCCT transporter	NA|257aa|down_6|CP022672.1_787932_788703_+	PRK03359, PRK03359, putative electron transfer flavoprotein FixA; Reviewed	NA|314aa|down_7|CP022672.1_788717_789659_+	PRK03363, fixB, electron transfer flavoprotein subunit alpha/FixB family protein	NA|429aa|down_8|CP022672.1_789709_790996_+	PRK10157, PRK10157, putative oxidoreductase FixC; Provisional	NA|96aa|down_9|CP022672.1_790992_791280_+	PRK15449, PRK15449, ferredoxin-like protein FixX; Provisional
GCA_003265245.1_ASM326524v1	CP022672	Shigella sonnei strain 866 chromosome, complete genome	2	787711-787842	1	PILER-CR	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11	Orphan	TTTTCAATATTGGTGAT	17	0	0	NA	NA	NA	2	2	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11,TnsE_C	NA,NA	NA|274aa|up_9|CP022672.1_771736_772558_+	COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism]	NA|383aa|up_8|CP022672.1_773013_774162_+	PRK12564, PRK12564, carbamoyl-phosphate synthase small subunit	NA|1074aa|up_7|CP022672.1_774179_777401_+	PRK05294, carB, carbamoyl-phosphate synthase large subunit	NA|132aa|up_6|CP022672.1_778438_778834_+	PRK11476, PRK11476, carnitine metabolism transcriptional regulator CaiF	NA|197aa|up_5|CP022672.1_779042_779633_-	PRK13627, PRK13627, carnitine operon protein CaiE; Provisional	NA|262aa|up_4|CP022672.1_779638_780424_-	PRK03580, PRK03580, crotonobetainyl-CoA hydratase	NA|518aa|up_3|CP022672.1_780532_782086_-	PRK08008, caiC, putative crotonobetaine/carnitine-CoA ligase; Validated	NA|386aa|up_2|CP022672.1_782249_783406_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|381aa|up_1|CP022672.1_784772_785915_-	PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated	NA|505aa|up_0|CP022672.1_785945_787460_-	PRK03356, PRK03356, L-carnitine/gamma-butyrobetaine antiport BCCT transporter	NA|257aa|down_0|CP022672.1_787932_788703_+	PRK03359, PRK03359, putative electron transfer flavoprotein FixA; Reviewed	NA|314aa|down_1|CP022672.1_788717_789659_+	PRK03363, fixB, electron transfer flavoprotein subunit alpha/FixB family protein	NA|429aa|down_2|CP022672.1_789709_790996_+	PRK10157, PRK10157, putative oxidoreductase FixC; Provisional	NA|96aa|down_3|CP022672.1_790992_791280_+	PRK15449, PRK15449, ferredoxin-like protein FixX; Provisional	NA|177aa|down_4|CP022672.1_792777_793308_+	PRK00871, PRK00871, glutathione-regulated potassium-efflux system oxidoreductase KefF	NA|621aa|down_5|CP022672.1_793300_795163_+	PRK03562, PRK03562, glutathione-regulated potassium-efflux system protein KefC; Provisional	NA|160aa|down_6|CP022672.1_795354_795834_+	PRK10769, folA, type 3 dihydrofolate reductase	NA|281aa|down_7|CP022672.1_795911_796754_-	TIGR00668, Bis5'-nucleosyl-tetraphosphatase_symmetrical, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)	NA|126aa|down_8|CP022672.1_796760_797138_-	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed	NA|274aa|down_9|CP022672.1_797140_797962_-	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA
GCA_003265245.1_ASM326524v1	CP022672	Shigella sonnei strain 866 chromosome, complete genome	3	1675336-1675484	2	CRISPRCasFinder	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11	Orphan	GTTCACTGCCGTACAGGCAGCTTAGAAAT	29	0	0	NA	NA	I-F	2	2	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11,TnsE_C	NA|82aa|up_7|CP022672.1_1668122_1668368_+,NA|65aa|up_5|CP022672.1_1669255_1669450_+,NA|85aa|up_4|CP022672.1_1671280_1671535_-,NA|94aa|up_3|CP022672.1_1671572_1671854_+,NA|82aa|up_2|CP022672.1_1672106_1672352_-,NA	NA|100aa|up_9|CP022672.1_1665720_1666020_+	pfam13973, DUF4222, Domain of unknown function (DUF4222)	NA|601aa|up_8|CP022672.1_1666016_1667819_+	COG3378, COG3378, Phage associated DNA primase [General function prediction only]	NA|82aa|up_7|CP022672.1_1668122_1668368_+	NA	NA|141aa|up_6|CP022672.1_1668364_1668787_+	cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB)	NA|65aa|up_5|CP022672.1_1669255_1669450_+	NA	NA|85aa|up_4|CP022672.1_1671280_1671535_-	NA	NA|94aa|up_3|CP022672.1_1671572_1671854_+	NA	NA|82aa|up_2|CP022672.1_1672106_1672352_-	NA	NA|107aa|up_1|CP022672.1_1672493_1672814_+	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|759aa|up_0|CP022672.1_1672844_1675121_+	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|73aa|down_0|CP022672.1_1675867_1676086_-	PRK00276, infA, translation initiation factor IF-1; Validated	NA|235aa|down_1|CP022672.1_1676370_1677075_-	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|574aa|down_2|CP022672.1_1677116_1678838_-	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|589aa|down_3|CP022672.1_1678838_1680605_-	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|322aa|down_4|CP022672.1_1680727_1681693_-	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|165aa|down_5|CP022672.1_1682237_1682732_+	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|1356aa|down_6|CP022672.1_1682866_1686934_+	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|204aa|down_7|CP022672.1_1687088_1687700_+	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|448aa|down_8|CP022672.1_1687710_1689054_+	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|431aa|down_9|CP022672.1_1689144_1690437_+	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional
GCA_003265245.1_ASM326524v1	CP022672	Shigella sonnei strain 866 chromosome, complete genome	4	2302304-2302427	3	CRISPRCasFinder	no	cas3,DEDDh	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11	Unclear	CGACCCCCACCATGTCAAGGTGGTGCTCTAACCAACTGAGCTA	43	0	0	NA	NA	NA	1	1	Unclear	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11,TnsE_C	NA,NA|75aa|down_7|CP022672.1_2311012_2311237_-,NA|30aa|down_8|CP022672.1_2311323_2311413_+	NA|471aa|up_9|CP022672.1_2291751_2293164_-	PRK09206, PRK09206, pyruvate kinase PykF	NA|70aa|up_8|CP022672.1_2293720_2293930_+	PRK10292, PRK10292, fumarate hydratase FumD	NA|209aa|up_7|CP022672.1_2294385_2295012_+	PRK09898, PRK09898, ferredoxin-like protein	NA|703aa|up_6|CP022672.1_2295032_2297141_+	PRK09849, PRK09849, putative oxidoreductase; Provisional	NA|216aa|up_5|CP022672.1_2297144_2297792_+	PRK09947, PRK09947, YdhW family putative oxidoreductase system protein	NA|223aa|up_4|CP022672.1_2297855_2298524_+	TIGR03149, cyt_nit_nrfC, cytochrome c nitrite reductase, Fe-S protein	NA|262aa|up_3|CP022672.1_2298520_2299306_+	PRK15006, PRK15006, thiosulfate reductase cytochrome B subunit; Provisional	NA|271aa|up_2|CP022672.1_2299309_2300122_+	PRK09946, PRK09946, hypothetical protein; Provisional	NA|535aa|up_1|CP022672.1_2300133_2301738_-	PRK09897, PRK09897, FAD-NAD(P)-binding protein	NA|102aa|up_0|CP022672.1_2301863_2302169_-	PRK11118, PRK11118, putative monooxygenase; Provisional	NA|419aa|down_0|CP022672.1_2302741_2303998_+	PRK09945, PRK09945, hypothetical protein; Provisional	NA|458aa|down_1|CP022672.1_2304038_2305412_-	PRK01766, PRK01766, multidrug efflux protein; Reviewed	NA|214aa|down_2|CP022672.1_2305626_2306268_+	PRK13020, PRK13020, riboflavin synthase subunit alpha; Provisional	NA|383aa|down_3|CP022672.1_2306307_2307456_-	PRK11705, PRK11705, cyclopropane fatty acyl phospholipid synthase	NA|404aa|down_4|CP022672.1_2307746_2308958_-	PRK11043, PRK11043, Bcr/CflA family multidrug efflux MFS transporter	NA|311aa|down_5|CP022672.1_2309070_2310003_+	PRK11074, PRK11074, putative DNA-binding transcriptional regulator; Provisional	NA|342aa|down_6|CP022672.1_2309999_2311025_-	PRK10703, PRK10703, HTH-type transcriptional repressor PurR	NA|75aa|down_7|CP022672.1_2311012_2311237_-	NA	NA|30aa|down_8|CP022672.1_2311323_2311413_+	NA	NA|390aa|down_9|CP022672.1_2311578_2312748_+	COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport and metabolism]
GCA_003265245.1_ASM326524v1	CP022672	Shigella sonnei strain 866 chromosome, complete genome	5	3183488-3183614	4	CRISPRCasFinder	no		DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11	Orphan	TTTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC	39	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11,TnsE_C	NA,NA|28aa|down_2|CP022672.1_3185837_3185921_-	NA|217aa|up_9|CP022672.1_3161855_3162506_+	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit	NA|441aa|up_8|CP022672.1_3162502_3163825_+	pfam02667, SCFA_trans, Short chain fatty acid transporter	NA|395aa|up_7|CP022672.1_3163855_3165040_+	PRK05790, PRK05790, putative acyltransferase; Provisional	NA|259aa|up_6|CP022672.1_3165113_3165890_-	COG4676, COG4676, Uncharacterized protein conserved in bacteria [Function unknown]	NA|550aa|up_5|CP022672.1_3165894_3167544_-	COG5445, COG5445, Predicted secreted protein [Function unknown]	NA|510aa|up_4|CP022672.1_3170006_3171536_-	COG4685, COG4685, Uncharacterized protein conserved in bacteria [Function unknown]	NA|876aa|up_3|CP022672.1_3171743_3174371_-	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|241aa|up_2|CP022672.1_3174517_3175240_+	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|425aa|up_1|CP022672.1_3178263_3179537_+	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|762aa|up_0|CP022672.1_3181151_3183437_+	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|377aa|down_0|CP022672.1_3183670_3184801_+	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|85aa|down_1|CP022672.1_3184800_3185055_+	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|28aa|down_2|CP022672.1_3185837_3185921_-	NA	NA|390aa|down_3|CP022672.1_3186820_3187989_+	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|47aa|down_4|CP022672.1_3188563_3188704_+	PRK09729, PRK09729, hypothetical protein; Provisional	NA|359aa|down_5|CP022672.1_3188745_3189822_-	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|453aa|down_6|CP022672.1_3189826_3191185_-	PRK11273, glpT, glycerol-3-phosphate transporter	NA|543aa|down_7|CP022672.1_3191457_3193086_+	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|420aa|down_8|CP022672.1_3193075_3194335_+	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|397aa|down_9|CP022672.1_3194331_3195522_+	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit
GCA_003265245.1_ASM326524v1	CP022673	Shigella sonnei strain 866 plasmid p866, complete sequence	1	84330-84421	1	CRISPRCasFinder	no	csa3,TnsE_C	csa3,TnsE_C	Type I-A	AAAGTGAAATTTCTTCACTTTTTCA	25	0	0	NA	NA	NA	1	1	Orphan	DEDDh,DinG,cas3,c2c9_V-U4,csa3,cas2,cas6e,cas5,cas7,cse2gr11,TnsE_C	NA|111aa|up_3|CP022673.1_82016_82349_-,NA|72aa|up_0|CP022673.1_83975_84191_-,NA|130aa|down_3|CP022673.1_85881_86271_-,NA|89aa|down_4|CP022673.1_86447_86714_-,NA|145aa|down_5|CP022673.1_86806_87241_-,NA|72aa|down_6|CP022673.1_87237_87453_-,NA|199aa|down_8|CP022673.1_88935_89532_-	NA|158aa|up_9|CP022673.1_75722_76196_-	cd00209, DHFR, Dihydrofolate reductase (DHFR)	NA|179aa|up_8|CP022673.1_76527_77064_+	TIGR02249, Integrase/recombinase_E2_protein	NA|109aa|up_7|CP022673.1_77178_77505_+	TIGR02249, Integrase/recombinase_E2_protein	NA|80aa|up_6|CP022673.1_77692_77932_-	pfam08849, DUF1819, Putative inner membrane protein (DUF1819)	NA|144aa|up_5|CP022673.1_78794_79226_-	pfam06519, TolA, TolA C-terminal	NA|904aa|up_4|CP022673.1_79293_82005_-	pfam03432, Relaxase, Relaxase/Mobilisation nuclease domain	NA|111aa|up_3|CP022673.1_82016_82349_-	NA	NA|112aa|up_2|CP022673.1_82581_82917_+	cd16149, sulfatase_like, uncharacterized sulfatase subfamily	NA|283aa|up_1|CP022673.1_83002_83851_-	pfam13708, DUF4942, Domain of unknown function (DUF4942)	NA|72aa|up_0|CP022673.1_83975_84191_-	NA	NA|84aa|down_0|CP022673.1_84431_84683_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|74aa|down_1|CP022673.1_84713_84935_-	TIGR01784, Uncharacterized_protein_pSLT051, conserved hypothetical protein (putative transposase or invertase)	NA|309aa|down_2|CP022673.1_84958_85885_-	PRK09956, PRK09956, ISNCY family transposase	NA|130aa|down_3|CP022673.1_85881_86271_-	NA	NA|89aa|down_4|CP022673.1_86447_86714_-	NA	NA|145aa|down_5|CP022673.1_86806_87241_-	NA	NA|72aa|down_6|CP022673.1_87237_87453_-	NA	NA|167aa|down_7|CP022673.1_87973_88474_-	pfam07275, ArdA, Antirestriction protein (ArdA)	NA|199aa|down_8|CP022673.1_88935_89532_-	NA	NA|240aa|down_9|CP022673.1_89528_90248_-	PRK13704, PRK13704, plasmid SOS inhibition protein A; Provisional
