Input and runtime details for job 1765463 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
51	0.009714	0.6129	b1736	chbA	-9.09	0.063099	186 -- 194	44 -- 52	N N'-diacetylchitobiose-specific enzyme IIA component of PTS	_____________185_______195\n_____________\|_________\|\n5'-GGU...AGAAA_________CGAUG...GCC-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	188 -- 194	44 -- 50	-11.469 kcal/mol	1.52278 kcal/mol	0.860683 kcal/mol	185 195@LB@ \| \|@LB@5'-GGU...AGAAA CGAUG...GCC-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -9.09 kcal/mol@LB@Hybridization Energy -11.469 kcal/mol@LB@Unfolding Energy - mRNA 1.52278 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
52	0.01005	0.6177	b3985	rplJ	-10.76	0.028819	17 -- 26	48 -- 57	50S ribosomal subunit protein L10	_____________16_________27\n_____________\|__________\|\n5'-UGG...GGCCU__________CCGCA...UAA-3'\n______________CCGUCGAAGA\n______________\|\|\|\|\|:\|\|\|\|\n______________GGCAGUUUCU\n3'-UUU...AACCG__________CCUUA...ACA-5'\n_____________\|__________\|\n_____________58_________47\n	20 -- 26	48 -- 54	-14.4896 kcal/mol	0.999171 kcal/mol	2.73483 kcal/mol	16 27@LB@ \| \|@LB@5'-UGG...GGCCU CCGCA...UAA-3'@LB@ CCGUCGAAGA@LB@ \|\|\|\|\|:\|\|\|\|@LB@ GGCAGUUUCU@LB@3'-UUU...AACCG CCUUA...ACA-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -14.4896 kcal/mol@LB@Unfolding Energy - mRNA 0.999171 kcal/mol@LB@Unfolding Energy - sRNA 2.73483 kcal/mol@LB@@LB@Position - mRNA 17 -- 26@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 48 -- 54@LB@
53	0.01077	0.6177	b3429	glgA	-6.74	0.182373	105 -- 111	44 -- 50	glycogen synthase	_____________104_____112\n_____________\|_______\|\n5'-GUA...AACGC_______GAUGC...ACG-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	105 -- 111	44 -- 50	-9.00959 kcal/mol	1.43957 kcal/mol	0.825028 kcal/mol	104 112@LB@ \| \|@LB@5'-GUA...AACGC GAUGC...ACG-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -6.74 kcal/mol@LB@Hybridization Energy -9.00959 kcal/mol@LB@Unfolding Energy - mRNA 1.43957 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 44 -- 50@LB@
54	0.01118	0.6177	b0127	yadG	-7.27	0.144346	282 -- 299	40 -- 55	putative ABC transporter ATPase	_____________281________________300\n_____________\|__________________\|\n5'-UGU...UGCAG_______C___U______U-3'\n______________GUCGAAG_GGG_GAUUUU\n______________\|\|\|:\|\|\|_:\|\|_:\|\|\|\|:\n______________CAGUUUC_UCC_UUAAAG\n3'-UUU...CCGGG__________________UAAAA...ACA-5'\n_____________\|__________________\|\n_____________56_________________39\n	282 -- 288	49 -- 55	-13.6497 kcal/mol	5.35692 kcal/mol	1.01784 kcal/mol	281 300@LB@ \| \|@LB@5'-UGU...UGCAG C U U-3'@LB@ GUCGAAG GGG GAUUUU@LB@ \|\|\|:\|\|\| :\|\| :\|\|\|\|:@LB@ CAGUUUC UCC UUAAAG@LB@3'-UUU...CCGGG UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -13.6497 kcal/mol@LB@Unfolding Energy - mRNA 5.35692 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 282 -- 299@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 49 -- 55@LB@
55	0.01149	0.6177	b3287	def	-9.61	0.049470	133 -- 146	41 -- 54	peptide deformylase	_____________132____________147\n_____________\|______________\|\n5'-AUA...GUCAA______________GUCUA...AUG-3'\n______________UCAGAGGGGGAUUU\n______________\|\|\|:\|\|:\|\|:\|\|\|\|\n______________AGUUUCUCCUUAAA\n3'-UUU...CGGGC______________GUAAA...ACA-5'\n_____________\|______________\|\n_____________55_____________40\n	140 -- 146	41 -- 47	-17.2173 kcal/mol	6.66439 kcal/mol	0.946064 kcal/mol	132 147@LB@ \| \|@LB@5'-AUA...GUCAA GUCUA...AUG-3'@LB@ UCAGAGGGGGAUUU@LB@ \|\|\|:\|\|:\|\|:\|\|\|\|@LB@ AGUUUCUCCUUAAA@LB@3'-UUU...CGGGC GUAAA...ACA-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -17.2173 kcal/mol@LB@Unfolding Energy - mRNA 6.66439 kcal/mol@LB@Unfolding Energy - sRNA 0.946064 kcal/mol@LB@@LB@Position - mRNA 133 -- 146@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 41 -- 47@LB@
56	0.01199	0.6177	b0836	bssR	-10.68	0.029916	18 -- 32	42 -- 55	repressor of biofilm formation by indole transport regulation	_____________17______________33\n_____________\|_______________\|\n5'-AUU...GAAAG_______C_______CUACA...ACA-3'\n______________GUCAGGG_AGGGAUU\n______________\|\|\|\|::\|_\|\|\|:\|\|\|\n______________CAGUUUC_UCCUUAA\n3'-UUU...CCGGG_______________AGUAA...ACA-5'\n_____________\|_______________\|\n_____________56______________41\n	26 -- 32	42 -- 48	-16.3055 kcal/mol	4.68166 kcal/mol	0.947316 kcal/mol	17 33@LB@ \| \|@LB@5'-AUU...GAAAG C CUACA...ACA-3'@LB@ GUCAGGG AGGGAUU@LB@ \|\|\|\|::\| \|\|\|:\|\|\|@LB@ CAGUUUC UCCUUAA@LB@3'-UUU...CCGGG AGUAA...ACA-5'@LB@ \| \|@LB@ 56 41@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -16.3055 kcal/mol@LB@Unfolding Energy - mRNA 4.68166 kcal/mol@LB@Unfolding Energy - sRNA 0.947316 kcal/mol@LB@@LB@Position - mRNA 18 -- 32@LB@Position - sRNA 42 -- 55@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 42 -- 48@LB@
57	0.01201	0.6177	b2959	yggL	-9.33	0.056423	82 -- 92	47 -- 57	DUF469 family protein	_____________81__________93\n_____________\|___________\|\n5'-GUA...AAAAC___________CAAUG...CAU-3'\n______________CUGUCAGAGAG\n______________\|:\|\|\|\|:\|\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	86 -- 92	47 -- 53	-15.1623 kcal/mol	3.10124 kcal/mol	2.73556 kcal/mol	81 93@LB@ \| \|@LB@5'-GUA...AAAAC CAAUG...CAU-3'@LB@ CUGUCAGAGAG@LB@ \|:\|\|\|\|:\|\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -15.1623 kcal/mol@LB@Unfolding Energy - mRNA 3.10124 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 82 -- 92@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 47 -- 53@LB@
58	0.01235	0.6177	b3903	rhaA	-9.27	0.057813	267 -- 276	46 -- 55	L-rhamnose isomerase	_____________266________277\n_____________\|__________\|\n5'-GCC...UUGAU__________CGCUG...UAC-3'\n______________GUCGAGGAGG\n______________\|\|\|:\|:\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	270 -- 276	46 -- 52	-15.3197 kcal/mol	5.12197 kcal/mol	0.924411 kcal/mol	266 277@LB@ \| \|@LB@5'-GCC...UUGAU CGCUG...UAC-3'@LB@ GUCGAGGAGG@LB@ \|\|\|:\|:\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.3197 kcal/mol@LB@Unfolding Energy - mRNA 5.12197 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 267 -- 276@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 46 -- 52@LB@
59	0.01284	0.6177	b3453	ugpB	-7.80	0.113752	247 -- 260	43 -- 56	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein	_____________246____________261\n_____________\|______________\|\n5'-UUC...ACUGG______U_______GCACA...UGG-3'\n______________CGUUAA_GGGGAAU\n______________\|\|\|:\|\|_\|:\|\|\|\|\|\n______________GCAGUU_CUCCUUA\n3'-UUU...ACCGG______U_______AAGUA...ACA-5'\n_____________\|______________\|\n_____________57_____________42\n	254 -- 260	43 -- 49	-14.4117 kcal/mol	5.65325 kcal/mol	0.953958 kcal/mol	246 261@LB@ \| \|@LB@5'-UUC...ACUGG U GCACA...UGG-3'@LB@ CGUUAA GGGGAAU@LB@ \|\|\|:\|\| \|:\|\|\|\|\|@LB@ GCAGUU CUCCUUA@LB@3'-UUU...ACCGG U AAGUA...ACA-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -14.4117 kcal/mol@LB@Unfolding Energy - mRNA 5.65325 kcal/mol@LB@Unfolding Energy - sRNA 0.953958 kcal/mol@LB@@LB@Position - mRNA 247 -- 260@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 43 -- 49@LB@
60	0.01286	0.6177	b4113	basR	-8.68	0.076010	6 -- 31	48 -- 75	response regulator in two-component regulatory system with BasS	_____________5____________________________32\n_____________\|____________________________\|\n______5'-CAGGU_______C____________________AUUAU...CGC-3'\n______________GCCGAUG_UGCUG_UGG_CUGUCGGAGG\n______________\|\|\|:\|\|:_:\|\|\|:_\|\|\|_\|:\|\|\|::\|\|:\n______________CGGUUAU_GCGAU_ACC_GGCAGUUUCU\n3'-UUU...UUUAC_______A_____A___G__________CCUUA...ACA-5'\n_____________\|____________________________\|\n_____________76___________________________47\n	25 -- 31	48 -- 54	-31.4034 kcal/mol	11.3837 kcal/mol	11.3355 kcal/mol	5 32@LB@ \| \|@LB@ 5'-CAGGU C AUUAU...CGC-3'@LB@ GCCGAUG UGCUG UGG CUGUCGGAGG@LB@ \|\|\|:\|\|: :\|\|\|: \|\|\| \|:\|\|\|::\|\|:@LB@ CGGUUAU GCGAU ACC GGCAGUUUCU@LB@3'-UUU...UUUAC A A G CCUUA...ACA-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -8.68 kcal/mol@LB@Hybridization Energy -31.4034 kcal/mol@LB@Unfolding Energy - mRNA 11.3837 kcal/mol@LB@Unfolding Energy - sRNA 11.3355 kcal/mol@LB@@LB@Position - mRNA 6 -- 31@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 48 -- 54@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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