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_004328985.1_ASM432898v1	CP035008	Shigella sonnei strain LC1477/18 chromosome, complete genome	1	1407457-1407574	1	CRISPRCasFinder	no		c2c9_V-U4,cas3,cas7,cas5,cas6e,cas2,csa3,DEDDh,DinG,TnsE_C	Orphan	CCGAGCCGTAGGCCGGATAAGGCGTTCACGC	31	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,cas7,cas5,cas6e,cas2,csa3,DEDDh,DinG,TnsE_C	NA,NA	NA|268aa|up_9|CP035008.1_1392422_1393226_+	PRK10128, PRK10128, 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional	NA|301aa|up_8|CP035008.1_1393266_1394169_-	PRK09956, PRK09956, ISNCY family transposase	NA|397aa|up_7|CP035008.1_1394361_1395552_-	TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase, anaerobic, C subunit	NA|420aa|up_6|CP035008.1_1395548_1396808_-	COG3075, GlpB, Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]	NA|543aa|up_5|CP035008.1_1396797_1398426_-	PRK11101, glpA, anaerobic glycerol-3-phosphate dehydrogenase subunit A	NA|453aa|up_4|CP035008.1_1398698_1400057_+	PRK11273, glpT, glycerol-3-phosphate transporter	NA|359aa|up_3|CP035008.1_1400061_1401138_+	PRK11143, glpQ, glycerophosphodiester phosphodiesterase; Provisional	NA|344aa|up_2|CP035008.1_1404115_1405147_+	pfam13358, DDE_3, DDE superfamily endonuclease	NA|85aa|up_1|CP035008.1_1405975_1406230_-	PRK10713, PRK10713, 2Fe-2S ferredoxin-like protein	NA|377aa|up_0|CP035008.1_1406229_1407360_-	PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed	NA|762aa|down_0|CP035008.1_1407593_1409879_-	PRK09103, PRK09103, ribonucleoside-diphosphate reductase subunit alpha	NA|425aa|down_1|CP035008.1_1411493_1412767_-	PRK09409, PRK09409, IS2 transposase TnpB; Reviewed	NA|241aa|down_2|CP035008.1_1415790_1416513_-	PRK05134, PRK05134, bifunctional 2-polyprenyl-6-hydroxyphenol methylase/3-demethylubiquinol 3-O-methyltransferase UbiG	NA|876aa|down_3|CP035008.1_1416659_1419287_+	PRK05560, PRK05560, DNA gyrase subunit A; Validated	NA|510aa|down_4|CP035008.1_1419494_1421024_+	COG4685, COG4685, Uncharacterized protein conserved in bacteria [Function unknown]	NA|550aa|down_5|CP035008.1_1423486_1425136_+	COG5445, COG5445, Predicted secreted protein [Function unknown]	NA|259aa|down_6|CP035008.1_1425140_1425917_+	COG4676, COG4676, Uncharacterized protein conserved in bacteria [Function unknown]	NA|395aa|down_7|CP035008.1_1425990_1427175_-	PRK05790, PRK05790, putative acyltransferase; Provisional	NA|420aa|down_8|CP035008.1_1427205_1428465_-	pfam02667, SCFA_trans, Short chain fatty acid transporter	NA|217aa|down_9|CP035008.1_1428461_1429112_-	TIGR02428, 3-oxoadipate_CoA-transferase_subunit_B, 3-oxoacid CoA-transferase, B subunit
GCA_004328985.1_ASM432898v1	CP035008	Shigella sonnei strain LC1477/18 chromosome, complete genome	3	2867709-2867857	3,1	CRISPRCasFinder,PILER-CR	no		c2c9_V-U4,cas3,cas7,cas5,cas6e,cas2,csa3,DEDDh,DinG,TnsE_C	Orphan	ATTTCTAAGCTGCCTGTACGGCAGTGAAC,ATTTCTAAGCTGCCTGTACGGCAGTGAAC	29,29	0	0	NA	NA	I-F:I-F	2,2	2	Orphan	c2c9_V-U4,cas3,cas7,cas5,cas6e,cas2,csa3,DEDDh,DinG,TnsE_C	NA,NA|82aa|down_2|CP035008.1_2870840_2871086_+,NA|94aa|down_3|CP035008.1_2871338_2871620_-,NA|65aa|down_4|CP035008.1_2873742_2873937_-,NA|82aa|down_6|CP035008.1_2874824_2875070_-,NA|107aa|down_9|CP035008.1_2878745_2879066_-	NA|431aa|up_9|CP035008.1_2852755_2854048_-	PRK05431, PRK05431, seryl-tRNA synthetase; Provisional	NA|448aa|up_8|CP035008.1_2854138_2855482_-	PRK13342, PRK13342, recombination factor protein RarA; Reviewed	NA|204aa|up_7|CP035008.1_2855492_2856104_-	TIGR00547, Outer-membrane_lipoprotein_carrier_protein, periplasmic chaperone LolA	NA|1356aa|up_6|CP035008.1_2856258_2860326_-	PRK10263, PRK10263, DNA translocase FtsK; Provisional	NA|165aa|up_5|CP035008.1_2860460_2860955_-	PRK11169, PRK11169, leucine-responsive transcriptional regulator Lrp	NA|322aa|up_4|CP035008.1_2861499_2862465_+	PRK10262, PRK10262, thioredoxin reductase; Provisional	NA|589aa|up_3|CP035008.1_2862587_2864354_+	PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|574aa|up_2|CP035008.1_2864354_2866076_+	PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed	NA|235aa|up_1|CP035008.1_2866117_2866822_+	PRK00301, aat, leucyl/phenylalanyl-tRNA--protein transferase; Reviewed	NA|73aa|up_0|CP035008.1_2867106_2867325_+	PRK00276, infA, translation initiation factor IF-1; Validated	NA|759aa|down_0|CP035008.1_2868071_2870348_-	PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional	NA|107aa|down_1|CP035008.1_2870378_2870699_-	PRK00033, clpS, ATP-dependent Clp protease adaptor protein ClpS; Reviewed	NA|82aa|down_2|CP035008.1_2870840_2871086_+	NA	NA|94aa|down_3|CP035008.1_2871338_2871620_-	NA	NA|65aa|down_4|CP035008.1_2873742_2873937_-	NA	NA|141aa|down_5|CP035008.1_2874405_2874828_-	cd04496, SSB_OBF, SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB)	NA|82aa|down_6|CP035008.1_2874824_2875070_-	NA	NA|386aa|down_7|CP035008.1_2875697_2876854_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|100aa|down_8|CP035008.1_2878439_2878739_-	pfam13973, DUF4222, Domain of unknown function (DUF4222)	NA|107aa|down_9|CP035008.1_2878745_2879066_-	NA
GCA_004328985.1_ASM432898v1	CP035008	Shigella sonnei strain LC1477/18 chromosome, complete genome	4	3016561-3016705	4	CRISPRCasFinder	no		c2c9_V-U4,cas3,cas7,cas5,cas6e,cas2,csa3,DEDDh,DinG,TnsE_C	Orphan	GTAGGTCGGATAAGATGCGCAAGCATCGCATCCGACAATAAGTGCCGGATGC	52	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,cas7,cas5,cas6e,cas2,csa3,DEDDh,DinG,TnsE_C	NA,NA|169aa|down_4|CP035008.1_3023042_3023549_-,NA|255aa|down_8|CP035008.1_3028230_3028995_-	NA|385aa|up_9|CP035008.1_3004612_3005767_-	PRK05958, PRK05958, 8-amino-7-oxononanoate synthase; Reviewed	NA|347aa|up_8|CP035008.1_3005763_3006804_-	PRK15108, PRK15108, biotin synthase; Provisional	NA|430aa|up_7|CP035008.1_3006890_3008180_+	PRK07986, PRK07986, adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated	NA|159aa|up_6|CP035008.1_3008238_3008715_+	PRK10257, PRK10257, putative kinase inhibitor protein; Provisional	NA|588aa|up_5|CP035008.1_3009296_3011060_+	PRK15370, PRK15370, type III secretion system effector E3 ubiquitin transferase SlrP	NA|60aa|up_4|CP035008.1_3011060_3011240_-	pfam02413, Caudo_TAP, Caudovirales tail fibre assembly protein, lambda gpK	NA|208aa|up_3|CP035008.1_3011239_3011863_-	pfam14301, DUF4376, Domain of unknown function (DUF4376)	NA|418aa|up_2|CP035008.1_3011813_3013067_-	pfam08400, phage_tail_N, Prophage tail fibre N-terminal	NA|257aa|up_1|CP035008.1_3014306_3015077_+	cd00800, INT_Lambda_C, C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase	NA|428aa|up_0|CP035008.1_3015211_3016495_+	PRK10531, PRK10531, putative acyl-CoA thioester hydrolase	NA|727aa|down_0|CP035008.1_3016728_3018909_-	PRK11413, PRK11413, putative hydratase; Provisional	NA|318aa|down_1|CP035008.1_3019863_3020817_+	cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold	NA|332aa|down_2|CP035008.1_3020857_3021853_-	PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional	NA|44aa|down_3|CP035008.1_3022112_3022244_-	cd03768, SR_ResInv, Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain	NA|169aa|down_4|CP035008.1_3023042_3023549_-	NA	NA|407aa|down_5|CP035008.1_3023552_3024773_-	pfam09979, DUF2213, Uncharacterized protein conserved in bacteria (DUF2213)	NA|248aa|down_6|CP035008.1_3024776_3025520_-	pfam04233, Phage_Mu_F, Phage Mu protein F like protein	NA|468aa|down_7|CP035008.1_3026876_3028280_-	pfam04466, Terminase_3, Phage terminase large subunit	NA|255aa|down_8|CP035008.1_3028230_3028995_-	NA	NA|170aa|down_9|CP035008.1_3029192_3029702_+	COG0586, DedA, Uncharacterized membrane-associated protein [Function unknown]
GCA_004328985.1_ASM432898v1	CP035008	Shigella sonnei strain LC1477/18 chromosome, complete genome	5	3754351-3754483	2	PILER-CR	no		c2c9_V-U4,cas3,cas7,cas5,cas6e,cas2,csa3,DEDDh,DinG,TnsE_C	Orphan	ATCACCAATATTGAAAA	17	0	0	NA	NA	NA	2	2	Orphan	c2c9_V-U4,cas3,cas7,cas5,cas6e,cas2,csa3,DEDDh,DinG,TnsE_C	NA,NA	NA|330aa|up_9|CP035008.1_3743244_3744234_+	PRK00232, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed	NA|274aa|up_8|CP035008.1_3744230_3745052_+	PRK00274, ksgA, 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA	NA|126aa|up_7|CP035008.1_3745054_3745432_+	PRK05461, apaG, CO2+/MG2+ efflux protein ApaG; Reviewed	NA|281aa|up_6|CP035008.1_3745438_3746281_+	TIGR00668, Bis5'-nucleosyl-tetraphosphatase_symmetrical, bis(5'-nucleosyl)-tetraphosphatase (symmetrical)	NA|621aa|up_5|CP035008.1_3747029_3748892_-	PRK03562, PRK03562, glutathione-regulated potassium-efflux system protein KefC; Provisional	NA|177aa|up_4|CP035008.1_3748884_3749415_-	PRK00871, PRK00871, glutathione-regulated potassium-efflux system oxidoreductase KefF	NA|96aa|up_3|CP035008.1_3750912_3751200_-	PRK15449, PRK15449, ferredoxin-like protein FixX; Provisional	NA|429aa|up_2|CP035008.1_3751196_3752483_-	PRK10157, PRK10157, putative oxidoreductase FixC; Provisional	NA|314aa|up_1|CP035008.1_3752533_3753475_-	PRK03363, fixB, electron transfer flavoprotein subunit alpha/FixB family protein	NA|257aa|up_0|CP035008.1_3753489_3754260_-	PRK03359, PRK03359, putative electron transfer flavoprotein FixA; Reviewed	NA|505aa|down_0|CP035008.1_3754733_3756248_+	PRK03356, PRK03356, L-carnitine/gamma-butyrobetaine antiport BCCT transporter	NA|381aa|down_1|CP035008.1_3756278_3757421_+	PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated	NA|518aa|down_2|CP035008.1_3760106_3761660_+	PRK08008, caiC, putative crotonobetaine/carnitine-CoA ligase; Validated	NA|262aa|down_3|CP035008.1_3761768_3762554_+	PRK03580, PRK03580, crotonobetainyl-CoA hydratase	NA|197aa|down_4|CP035008.1_3762559_3763150_+	PRK13627, PRK13627, carnitine operon protein CaiE; Provisional	NA|132aa|down_5|CP035008.1_3763358_3763754_-	PRK11476, PRK11476, carnitine metabolism transcriptional regulator CaiF	NA|1074aa|down_6|CP035008.1_3764791_3768013_-	PRK05294, carB, carbamoyl-phosphate synthase large subunit	NA|383aa|down_7|CP035008.1_3768030_3769179_-	PRK12564, PRK12564, carbamoyl-phosphate synthase small subunit	NA|274aa|down_8|CP035008.1_3769634_3770456_-	COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism]	NA|305aa|down_9|CP035008.1_3770622_3771537_-	PRK10768, PRK10768, ribonucleoside hydrolase RihC; Provisional
GCA_004328985.1_ASM432898v1	CP035008	Shigella sonnei strain LC1477/18 chromosome, complete genome	6	3763188-3763317	5	CRISPRCasFinder	no		c2c9_V-U4,cas3,cas7,cas5,cas6e,cas2,csa3,DEDDh,DinG,TnsE_C	Orphan	GCTGGAGAGCAACCGTAGGCCGGATAAGATGCGCCAGCAT	40	0	0	NA	NA	NA	1	1	Orphan	c2c9_V-U4,cas3,cas7,cas5,cas6e,cas2,csa3,DEDDh,DinG,TnsE_C	NA,NA	NA|177aa|up_9|CP035008.1_3748884_3749415_-	PRK00871, PRK00871, glutathione-regulated potassium-efflux system oxidoreductase KefF	NA|96aa|up_8|CP035008.1_3750912_3751200_-	PRK15449, PRK15449, ferredoxin-like protein FixX; Provisional	NA|429aa|up_7|CP035008.1_3751196_3752483_-	PRK10157, PRK10157, putative oxidoreductase FixC; Provisional	NA|314aa|up_6|CP035008.1_3752533_3753475_-	PRK03363, fixB, electron transfer flavoprotein subunit alpha/FixB family protein	NA|257aa|up_5|CP035008.1_3753489_3754260_-	PRK03359, PRK03359, putative electron transfer flavoprotein FixA; Reviewed	NA|505aa|up_4|CP035008.1_3754733_3756248_+	PRK03356, PRK03356, L-carnitine/gamma-butyrobetaine antiport BCCT transporter	NA|381aa|up_3|CP035008.1_3756278_3757421_+	PRK03354, PRK03354, crotonobetainyl-CoA dehydrogenase; Validated	NA|518aa|up_2|CP035008.1_3760106_3761660_+	PRK08008, caiC, putative crotonobetaine/carnitine-CoA ligase; Validated	NA|262aa|up_1|CP035008.1_3761768_3762554_+	PRK03580, PRK03580, crotonobetainyl-CoA hydratase	NA|197aa|up_0|CP035008.1_3762559_3763150_+	PRK13627, PRK13627, carnitine operon protein CaiE; Provisional	NA|132aa|down_0|CP035008.1_3763358_3763754_-	PRK11476, PRK11476, carnitine metabolism transcriptional regulator CaiF	NA|1074aa|down_1|CP035008.1_3764791_3768013_-	PRK05294, carB, carbamoyl-phosphate synthase large subunit	NA|383aa|down_2|CP035008.1_3768030_3769179_-	PRK12564, PRK12564, carbamoyl-phosphate synthase small subunit	NA|274aa|down_3|CP035008.1_3769634_3770456_-	COG0289, DapB, Dihydrodipicolinate reductase [Amino acid transport and metabolism]	NA|305aa|down_4|CP035008.1_3770622_3771537_-	PRK10768, PRK10768, ribonucleoside hydrolase RihC; Provisional	NA|317aa|down_5|CP035008.1_3771602_3772553_-	PRK01045, ispH, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed	NA|150aa|down_6|CP035008.1_3772554_3773004_-	PRK15095, PRK15095, FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional	NA|165aa|down_7|CP035008.1_3773128_3773623_-	PRK00376, lspA, lipoprotein signal peptidase	NA|939aa|down_8|CP035008.1_3773622_3776439_-	PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed	NA|314aa|down_9|CP035008.1_3776481_3777423_-	PRK05627, PRK05627, bifunctional riboflavin kinase/FAD synthetase
