Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
35	0.0006725	0.06313	b3455	livG	-12.92	0.040223	97 -- 112	32 -- 46	branched-chain amino acid ABC transporter ATPase	_____________96_______________113\n_____________\|________________\|\n5'-AUG...UGCUC________GA______UGAUG...UCG-3'\n______________GGUGGUUU__UGGUGC\n______________\|\|\|\|\|\|\|:__\|\|\|\|:\|\n______________CCACCAAG__ACCAUG\n3'-UUU...UUCCU________G_______UCGAU...UCG-5'\n_____________\|________________\|\n_____________47_______________31\n	98 -- 104	39 -- 45	-21.8288 kcal/mol	5.65514 kcal/mol	3.25632 kcal/mol	96 113@LB@ \| \|@LB@5'-AUG...UGCUC GA UGAUG...UCG-3'@LB@ GGUGGUUU UGGUGC@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\|@LB@ CCACCAAG ACCAUG@LB@3'-UUU...UUCCU G UCGAU...UCG-5'@LB@ \| \|@LB@ 47 31@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -21.8288 kcal/mol@LB@Unfolding Energy - mRNA 5.65514 kcal/mol@LB@Unfolding Energy - sRNA 3.25632 kcal/mol@LB@@LB@Position - mRNA 97 -- 112@LB@Position - sRNA 32 -- 46@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 39 -- 45@LB@
32	0.0005297	0.05563	b3456	livM	-14.95	0.011565	245 -- 274	15 -- 42	branched-chain amino acid ABC transporter permease	_____________244____________________________275\n_____________\|______________________________\|\n5'-GCC...GCGAU______U____U___G_____C________CGUGC...CCA-3'\n______________GUUCUU_GUGC_GGC_GGCGU_UUUAUGGG\n______________\|\|\|\|:\|_\|\|:\|_:\|\|_:\|\|:\|_\|\|\|\|\|\|\|\|\n______________CAAGGA_CAUG_UCG_UCGUA_AAAUACCC\n3'-UUU...UCCAC______C________A______________AAUAC...UCG-5'\n_____________\|______________________________\|\n_____________43_____________________________14\n	268 -- 274	15 -- 21	-29.6256 kcal/mol	10.1077 kcal/mol	4.57031 kcal/mol	244 275@LB@ \| \|@LB@5'-GCC...GCGAU U U G C CGUGC...CCA-3'@LB@ GUUCUU GUGC GGC GGCGU UUUAUGGG@LB@ \|\|\|\|:\| \|\|:\| :\|\| :\|\|:\| \|\|\|\|\|\|\|\|@LB@ CAAGGA CAUG UCG UCGUA AAAUACCC@LB@3'-UUU...UCCAC C A AAUAC...UCG-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -14.95 kcal/mol@LB@Hybridization Energy -29.6256 kcal/mol@LB@Unfolding Energy - mRNA 10.1077 kcal/mol@LB@Unfolding Energy - sRNA 4.57031 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 15 -- 21@LB@
198	0.01161	0.1971	b2712	hypF	-10.23	0.151482	281 -- 290	24 -- 33	carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein	_____________280________291\n_____________\|__________\|\n5'-GAA...GUCUG__________CAGCA...UAA-3'\n______________GCAGCUGGCA\n______________:\|\|\|\|\|:\|\|\|\n______________UGUCGAUCGU\n3'-UUU...GACCA__________AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	284 -- 290	24 -- 30	-16.4359 kcal/mol	4.77953 kcal/mol	1.42716 kcal/mol	280 291@LB@ \| \|@LB@5'-GAA...GUCUG CAGCA...UAA-3'@LB@ GCAGCUGGCA@LB@ :\|\|\|\|\|:\|\|\|@LB@ UGUCGAUCGU@LB@3'-UUU...GACCA AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -16.4359 kcal/mol@LB@Unfolding Energy - mRNA 4.77953 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 281 -- 290@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 24 -- 30@LB@
69	0.001909	0.09081	b1830	prc	-10.38	0.141777	185 -- 217	2 -- 49	carboxy-terminal protease for penicillin-binding protein 3	_____________184______________________________________________218\n_____________\|________________________________________________\|\n5'-CGA...GAAAC_______________GC__________GAAC_________________GCUUA...CGG-3'\n______________GGAGG_____CC_GG__CAG___GCAU__________AUGUUUUUUAG\n______________\|\|\|\|\|_____\|\|_\|\|__\|\|\|___\|\|\|\|__________\|\|\|\|\|\|\|\|:\|\|\n______________CCUCC_____GG_CC__GUC___CGUA__________UACAAAAAGUC\n3'-UUU...CGAUU_____ACCAA__A__AU___GAU____AAAUACCCAA___________G-5'\n_____________\|________________________________________________\|\n_____________50_______________________________________________1\n	211 -- 217	2 -- 8	-24.9215 kcal/mol	9.93043 kcal/mol	4.60955 kcal/mol	184 218@LB@ \| \|@LB@5'-CGA...GAAAC GC GAAC GCUUA...CGG-3'@LB@ GGAGG CC GG CAG GCAU AUGUUUUUUAG@LB@ \|\|\|\|\| \|\| \|\| \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|:\|\|@LB@ CCUCC GG CC GUC CGUA UACAAAAAGUC@LB@3'-UUU...CGAUU ACCAA A AU GAU AAAUACCCAA G-5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -24.9215 kcal/mol@LB@Unfolding Energy - mRNA 9.93043 kcal/mol@LB@Unfolding Energy - sRNA 4.60955 kcal/mol@LB@@LB@Position - mRNA 185 -- 217@LB@Position - sRNA 2 -- 49@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 2 -- 8@LB@
41	0.0008276	0.06626	b1218	chaC	-8.54	0.293650	119 -- 139	24 -- 45	cation transport regulator	_____________118____________________140\n_____________\|______________________\|\n5'-AUA...CGUUA________AAAAUG________AAAAU...CGC-3'\n______________GUGGUUUC______AGC_AGUA\n______________\|\|\|\|\|\|:\|______\|\|\|_\|\|:\|\n______________CACCAAGG______UCG_UCGU\n3'-UUU...UCCUC________ACCAUG___A____AAAAU...UCG-5'\n_____________\|______________________\|\n_____________46_____________________23\n	120 -- 126	38 -- 44	-17.6586 kcal/mol	4.55792 kcal/mol	4.55794 kcal/mol	118 140@LB@ \| \|@LB@5'-AUA...CGUUA AAAAUG AAAAU...CGC-3'@LB@ GUGGUUUC AGC AGUA@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|:\|@LB@ CACCAAGG UCG UCGU@LB@3'-UUU...UCCUC ACCAUG A AAAAU...UCG-5'@LB@ \| \|@LB@ 46 23@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -17.6586 kcal/mol@LB@Unfolding Energy - mRNA 4.55792 kcal/mol@LB@Unfolding Energy - sRNA 4.55794 kcal/mol@LB@@LB@Position - mRNA 119 -- 139@LB@Position - sRNA 24 -- 45@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 38 -- 44@LB@
66	0.001771	0.09017	b0924	mukB	-12.08	0.063147	4 -- 24	1 -- 22	chromosome condensin MukBEF ATPase and DNA-binding subunit	_____________3______________________25\n_____________\|______________________\|\n________5'-UGG________CCACGACAG_____AAGUU...CUG-3'\n______________UUUAUGGG__________CAGC\n______________\|\|\|\|\|\|\|\|__________\|\|\|\|\n______________AAAUACCC__________GUCG\n3'-UUU...UCGUA________AAUACAAAAA____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	5 -- 11	15 -- 21	-14.8798 kcal/mol	1.84387 kcal/mol	0.958674 kcal/mol	3 25@LB@ \| \|@LB@ 5'-UGG CCACGACAG AAGUU...CUG-3'@LB@ UUUAUGGG CAGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|@LB@ AAAUACCC GUCG@LB@3'-UUU...UCGUA AAUACAAAAA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -14.8798 kcal/mol@LB@Unfolding Energy - mRNA 1.84387 kcal/mol@LB@Unfolding Energy - sRNA 0.958674 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 15 -- 21@LB@
62	0.00164	0.08891	b0922	mukF	-17.51	0.001582	1 -- 30	14 -- 38	chromosome condensin MukBEF kleisin-like subunit binds calcium	______________1_____________________________31\n______________\|_____________________________\|\n___________5'-____AAGAA__U________AA________AAGAC...UGG-3'\n______________CUGG_____GC_GGUUGGCA__UUAUGGGU\n______________\|\|\|\|_____:\|_:\|:\|:\|\|\|__\|\|\|\|\|\|\|\|\n______________GACC_____UG_UCGAUCGU__AAUACCCA\n3'-UUU...CCAAG____A_______________AA________AUACA...UCG-5'\n_____________\|______________________________\|\n_____________39_____________________________13\n	24 -- 30	14 -- 20	-25.2653 kcal/mol	3.2564 kcal/mol	4.5012 kcal/mol	1 31@LB@ \| \|@LB@ 5'- AAGAA U AA AAGAC...UGG-3'@LB@ CUGG GC GGUUGGCA UUAUGGGU@LB@ \|\|\|\| :\| :\|:\|:\|\|\| \|\|\|\|\|\|\|\|@LB@ GACC UG UCGAUCGU AAUACCCA@LB@3'-UUU...CCAAG A AA AUACA...UCG-5'@LB@ \| \|@LB@ 39 13@LB@@LB@@LB@Energy -17.51 kcal/mol@LB@Hybridization Energy -25.2653 kcal/mol@LB@Unfolding Energy - mRNA 3.2564 kcal/mol@LB@Unfolding Energy - sRNA 4.5012 kcal/mol@LB@@LB@Position - mRNA 1 -- 30@LB@Position - sRNA 14 -- 38@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 14 -- 20@LB@
141	0.006623	0.1579	b1992	cobS	-16.13	0.004945	167 -- 192	24 -- 49	cobalamin synthase	_____________166_________________________193\n_____________\|___________________________\|\n5'-GAG...AGUAU__CU_________G_____UGG_____AAAAU...GUA-3'\n______________GG__GGUGGUUUC_GGUAU____AGUA\n______________\|\|__\|\|\|\|\|\|\|:\|_\|\|\|\|:____\|\|:\|\n______________CC__CCACCAAGG_CCAUG____UCGU\n3'-UUU...CGAUU__U__________A_____UCGA____AAAAU...UCG-5'\n_____________\|___________________________\|\n_____________50__________________________23\n	173 -- 179	38 -- 44	-26.3933 kcal/mol	5.70356 kcal/mol	4.5591 kcal/mol	166 193@LB@ \| \|@LB@5'-GAG...AGUAU CU G UGG AAAAU...GUA-3'@LB@ GG GGUGGUUUC GGUAU AGUA@LB@ \|\| \|\|\|\|\|\|\|:\| \|\|\|\|: \|\|:\|@LB@ CC CCACCAAGG CCAUG UCGU@LB@3'-UUU...CGAUU U A UCGA AAAAU...UCG-5'@LB@ \| \|@LB@ 50 23@LB@@LB@@LB@Energy -16.13 kcal/mol@LB@Hybridization Energy -26.3933 kcal/mol@LB@Unfolding Energy - mRNA 5.70356 kcal/mol@LB@Unfolding Energy - sRNA 4.5591 kcal/mol@LB@@LB@Position - mRNA 167 -- 192@LB@Position - sRNA 24 -- 49@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 38 -- 44@LB@
54	0.001244	0.07744	b1874	cutC	-11.77	0.073856	3 -- 15	22 -- 35	copper homeostasis protein	_____________2______________16\n_____________\|______________\|\n_________5'-CC______________GCUUU...AGG-3'\n______________GUGC_GCUGGCAUU\n______________\|\|:\|_\|\|\|:\|\|\|\|\|\n______________CAUG_CGAUCGUAA\n3'-UUU...AGGAC____U_________AAUAC...UCG-5'\n_____________\|______________\|\n_____________36_____________21\n	9 -- 15	22 -- 28	-17.4456 kcal/mol	4.24515 kcal/mol	1.43095 kcal/mol	2 16@LB@ \| \|@LB@ 5'-CC GCUUU...AGG-3'@LB@ GUGC GCUGGCAUU@LB@ \|\|:\| \|\|\|:\|\|\|\|\|@LB@ CAUG CGAUCGUAA@LB@3'-UUU...AGGAC U AAUAC...UCG-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -17.4456 kcal/mol@LB@Unfolding Energy - mRNA 4.24515 kcal/mol@LB@Unfolding Energy - sRNA 1.43095 kcal/mol@LB@@LB@Position - mRNA 3 -- 15@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 22 -- 28@LB@
163	0.008426	0.1737	b2780	pyrG	-11.06	0.104451	98 -- 140	14 -- 51	CTP synthetase	_____________97_____________________________________________141\n_____________\|______________________________________________\|\n5'-UGU...GCGAA_______GAUAAUGAAA____G___C____G______GUUC_____AUACU...GCC-3'\n______________GAGGAGG__________GUUU_UGG_ACAG_U__CAU_____GGGU\n______________:\|\|\|\|\|\|__________\|\|\|:_\|\|\|_\|\|\|\|_\|__\|\|\|_____\|\|\|\|\n______________UUCCUCC__________CAAG_ACC_UGUC_A__GUA_____CCCA\n3'-UUU...UCCGA_______AC____________G___A____G_UC___AAAUA____AUACA...UCG-5'\n_____________\|______________________________________________\|\n_____________52_____________________________________________13\n	98 -- 104	45 -- 51	-28.7226 kcal/mol	13.0099 kcal/mol	4.65749 kcal/mol	97 141@LB@ \| \|@LB@5'-UGU...GCGAA GAUAAUGAAA G C G GUUC AUACU...GCC-3'@LB@ GAGGAGG GUUU UGG ACAG U CAU GGGU@LB@ :\|\|\|\|\|\| \|\|\|: \|\|\| \|\|\|\| \| \|\|\| \|\|\|\|@LB@ UUCCUCC CAAG ACC UGUC A GUA CCCA@LB@3'-UUU...UCCGA AC G A G UC AAAUA AUACA...UCG-5'@LB@ \| \|@LB@ 52 13@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -28.7226 kcal/mol@LB@Unfolding Energy - mRNA 13.0099 kcal/mol@LB@Unfolding Energy - sRNA 4.65749 kcal/mol@LB@@LB@Position - mRNA 98 -- 140@LB@Position - sRNA 14 -- 51@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 45 -- 51@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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