Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
57	0.0008523	0.0526	b3281	aroE	-7.63	0.189523	225 -- 232	52 -- 59	dehydroshikimate reductase NAD(P)-binding	_____________224______233\n_____________\|________\|\n5'-UUU...UUGGU________AGCCC...AUG-3'\n______________AAUCCGAU\n______________\|\|\|\|\|\|\|\|\n______________UUAGGCUA\n3'-AUU...UCGGU________AUGCA...AUG-5'\n_____________\|________\|\n_____________60_______51\n	226 -- 232	52 -- 58	-9.52512 kcal/mol	1.61129 kcal/mol	0.296943 kcal/mol	224 233@LB@ \| \|@LB@5'-UUU...UUGGU AGCCC...AUG-3'@LB@ AAUCCGAU@LB@ \|\|\|\|\|\|\|\|@LB@ UUAGGCUA@LB@3'-AUU...UCGGU AUGCA...AUG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -9.52512 kcal/mol@LB@Unfolding Energy - mRNA 1.61129 kcal/mol@LB@Unfolding Energy - sRNA 0.296943 kcal/mol@LB@@LB@Position - mRNA 225 -- 232@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 52 -- 58@LB@
127	0.004255	0.1179	b2838	lysA	-9.87	0.049362	214 -- 233	52 -- 69	diaminopimelate decarboxylase PLP-binding	_____________213__________________234\n_____________\|____________________\|\n5'-GGU...UUCAC________A_C___A_____CUCAC...CGC-3'\n______________UGUUCAGC_C_GAU_CCGAU\n______________\|:\|\|\|\|\|\|_\|_:\|\|_\|\|\|\|\|\n______________AUAAGUCG_G_UUA_GGCUA\n3'-AUU...AUUUU__________U_________AUGCA...AUG-5'\n_____________\|____________________\|\n_____________70___________________51\n	215 -- 221	62 -- 68	-18.1264 kcal/mol	2.0842 kcal/mol	6.19243 kcal/mol	213 234@LB@ \| \|@LB@5'-GGU...UUCAC A C A CUCAC...CGC-3'@LB@ UGUUCAGC C GAU CCGAU@LB@ \|:\|\|\|\|\|\| \| :\|\| \|\|\|\|\|@LB@ AUAAGUCG G UUA GGCUA@LB@3'-AUU...AUUUU U AUGCA...AUG-5'@LB@ \| \|@LB@ 70 51@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -18.1264 kcal/mol@LB@Unfolding Energy - mRNA 2.0842 kcal/mol@LB@Unfolding Energy - sRNA 6.19243 kcal/mol@LB@@LB@Position - mRNA 214 -- 233@LB@Position - sRNA 52 -- 69@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 62 -- 68@LB@
16	5.617e-05	0.01183	b0116	lpd	-12.59	0.006546	264 -- 293	29 -- 63	dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase	_____________263__________________________________294\n_____________\|____________________________________\|\n5'-CCG...CCGCU___U____________C___UUU_____________ACCGUAA-3'\n______________GCC___UCCG_UUGCG_UGA______AGGUCUGGAA\n______________\|\|\|___\|\|\|\|_\|\|:\|\|_\|\|\|______\|\|\|\|\|\|\|:\|\|\n______________CGG___AGGC_AAUGC_ACU______UCCAGACUUU\n3'-AUU...UAAGU___UUU____U_________UCAUUU__________CUAUC...AUG-5'\n_____________\|____________________________________\|\n_____________64___________________________________28\n	286 -- 292	30 -- 36	-30.8342 kcal/mol	7.36676 kcal/mol	10.8887 kcal/mol	263 294@LB@ \| \|@LB@5'-CCG...CCGCU U C UUU ACCGUAA-3'@LB@ GCC UCCG UUGCG UGA AGGUCUGGAA@LB@ \|\|\| \|\|\|\| \|\|:\|\| \|\|\| \|\|\|\|\|\|\|:\|\|@LB@ CGG AGGC AAUGC ACU UCCAGACUUU@LB@3'-AUU...UAAGU UUU U UCAUUU CUAUC...AUG-5'@LB@ \| \|@LB@ 64 28@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -30.8342 kcal/mol@LB@Unfolding Energy - mRNA 7.36676 kcal/mol@LB@Unfolding Energy - sRNA 10.8887 kcal/mol@LB@@LB@Position - mRNA 264 -- 293@LB@Position - sRNA 29 -- 63@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 30 -- 36@LB@
132	0.004657	0.1239	b1200	dhaK	-7.52	0.201505	172 -- 179	1 -- 8	dihydroxyacetone kinase PTS-dependent dihydroxyacetone-binding subunit	_____________171______180\n_____________\|________\|\n5'-UUC...AUCCA________CGUAA...UGU-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	173 -- 179	1 -- 7	-12.1513 kcal/mol	2.5392 kcal/mol	2.11603 kcal/mol	171 180@LB@ \| \|@LB@5'-UUC...AUCCA CGUAA...UGU-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -12.1513 kcal/mol@LB@Unfolding Energy - mRNA 2.5392 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 172 -- 179@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
162	0.006534	0.1413	b3771	ilvD	-6.87	0.280008	44 -- 51	49 -- 56	dihydroxyacid dehydratase	_____________43_______52\n_____________\|________\|\n5'-GCG...GUGGC________CAAAC...GUA-3'\n______________CCGGUUAC\n______________\|\|\|:\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	45 -- 51	49 -- 55	-9.72973 kcal/mol	2.55538 kcal/mol	0.317884 kcal/mol	43 52@LB@ \| \|@LB@5'-GCG...GUGGC CAAAC...GUA-3'@LB@ CCGGUUAC@LB@ \|\|\|:\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -6.87 kcal/mol@LB@Hybridization Energy -9.72973 kcal/mol@LB@Unfolding Energy - mRNA 2.55538 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 44 -- 51@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 49 -- 55@LB@
90	0.002406	0.09404	b0551	quuD	-13.47	0.003063	177 -- 196	40 -- 58	DLP12 prophage; putative antitermination protein	_____________176__________________197\n_____________\|____________________\|\n5'-ACU...UUCUG________UU__________GUUGA...GAU-3'\n______________GUCUGAUU__UGUGGAGUAA\n______________:\|\|:\|\|\|\|__:\|\|\|:\|\|\|\|\|\n______________UAGGCUAA__GCACUUCAUU\n3'-AUU...CGGUU________U___________UUCCA...AUG-5'\n_____________\|____________________\|\n_____________59___________________39\n	190 -- 196	40 -- 46	-19.625 kcal/mol	2.82746 kcal/mol	3.34877 kcal/mol	176 197@LB@ \| \|@LB@5'-ACU...UUCUG UU GUUGA...GAU-3'@LB@ GUCUGAUU UGUGGAGUAA@LB@ :\|\|:\|\|\|\| :\|\|\|:\|\|\|\|\|@LB@ UAGGCUAA GCACUUCAUU@LB@3'-AUU...CGGUU U UUCCA...AUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -19.625 kcal/mol@LB@Unfolding Energy - mRNA 2.82746 kcal/mol@LB@Unfolding Energy - sRNA 3.34877 kcal/mol@LB@@LB@Position - mRNA 177 -- 196@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
55	0.0008105	0.05184	b3262	yhdJ	-10.49	0.032282	53 -- 83	1 -- 34	DNA adenine methyltransferase SAM-dependent	_____________52_________________________________84\n_____________\|__________________________________\|\n5'-CCU...CUGCG____U____________A____GUG____G____GUAAA...GUG-3'\n______________CUGA__GAU_GGGCAUC__ACC___GUAC_CUGC\n______________\|\|\|\|__\|\|\|_\|::\|\|\|\|__\|\|\|___\|\|\|\|_\|\|:\|\n______________GACU__CUA_CUUGUAG__UGG___CAUG_GAUG\n3'-AUU...UUCCA____UU___U_______AA___AGA____G____-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	61 -- 67	18 -- 24	-29.8286 kcal/mol	10.2122 kcal/mol	9.14469 kcal/mol	52 84@LB@ \| \|@LB@5'-CCU...CUGCG U A GUG G GUAAA...GUG-3'@LB@ CUGA GAU GGGCAUC ACC GUAC CUGC@LB@ \|\|\|\| \|\|\| \|::\|\|\|\| \|\|\| \|\|\|\| \|\|:\|@LB@ GACU CUA CUUGUAG UGG CAUG GAUG@LB@3'-AUU...UUCCA UU U AA AGA G -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -29.8286 kcal/mol@LB@Unfolding Energy - mRNA 10.2122 kcal/mol@LB@Unfolding Energy - sRNA 9.14469 kcal/mol@LB@@LB@Position - mRNA 53 -- 83@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 18 -- 24@LB@
72	0.001216	0.05856	b3699	gyrB	-10.53	0.031588	1 -- 17	9 -- 25	DNA gyrase subunit B	______________1________________18\n______________\|________________\|\n___________5'-___UG____________AGCUU...GCA-3'\n______________AGA__AUUUUGCCUCUG\n______________\|\|\|__\|\|:\|\|:\|\|\|\|\|\|\n______________UCU__UAGAAUGGAGAC\n3'-AUU...UUCUA___UG____________AUGGGAUG-5'\n_____________\|_________________\|\n_____________26________________8\n	11 -- 17	9 -- 15	-19.3204 kcal/mol	1.07855 kcal/mol	7.71376 kcal/mol	1 18@LB@ \| \|@LB@ 5'- UG AGCUU...GCA-3'@LB@ AGA AUUUUGCCUCUG@LB@ \|\|\| \|\|:\|\|:\|\|\|\|\|\|@LB@ UCU UAGAAUGGAGAC@LB@3'-AUU...UUCUA UG AUGGGAUG-5'@LB@ \| \|@LB@ 26 8@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -19.3204 kcal/mol@LB@Unfolding Energy - mRNA 1.07855 kcal/mol@LB@Unfolding Energy - sRNA 7.71376 kcal/mol@LB@@LB@Position - mRNA 1 -- 17@LB@Position - sRNA 9 -- 25@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 9 -- 15@LB@
52	0.0006736	0.04557	b3964	yijD	-9.23	0.074829	177 -- 192	43 -- 57	DUF1422 family inner membrane protein	_____________176______________193\n_____________\|________________\|\n5'-ACU...AUUAU_____GAA________GACGA...UGC-3'\n______________UCCGG___AUGUGAAG\n______________\|\|\|\|:___\|:\|\|\|\|\|\|\n______________AGGCU___UGCACUUC\n3'-AUU...GGUUU_____AA_________AUUUU...AUG-5'\n_____________\|________________\|\n_____________58_______________42\n	186 -- 192	43 -- 49	-16.7307 kcal/mol	4.24116 kcal/mol	3.27382 kcal/mol	176 193@LB@ \| \|@LB@5'-ACU...AUUAU GAA GACGA...UGC-3'@LB@ UCCGG AUGUGAAG@LB@ \|\|\|\|: \|:\|\|\|\|\|\|@LB@ AGGCU UGCACUUC@LB@3'-AUU...GGUUU AA AUUUU...AUG-5'@LB@ \| \|@LB@ 58 42@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -16.7307 kcal/mol@LB@Unfolding Energy - mRNA 4.24116 kcal/mol@LB@Unfolding Energy - sRNA 3.27382 kcal/mol@LB@@LB@Position - mRNA 177 -- 192@LB@Position - sRNA 43 -- 57@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 43 -- 49@LB@
64	0.001083	0.05856	b3471	yhhQ	-11.41	0.016564	49 -- 60	44 -- 55	DUF165 family inner membrane protein	_____________48___________61\n_____________\|____________\|\n5'-AAA...GUUAA____________AAUUA...UUC-3'\n______________CGAUUGCGUGAA\n______________\|\|\|\|\|:\|\|\|\|\|\|\n______________GCUAAUGCACUU\n3'-AUU...UUUAG____________CAUUU...AUG-5'\n_____________\|____________\|\n_____________56___________43\n	54 -- 60	44 -- 50	-16.5289 kcal/mol	2.50651 kcal/mol	2.62518 kcal/mol	48 61@LB@ \| \|@LB@5'-AAA...GUUAA AAUUA...UUC-3'@LB@ CGAUUGCGUGAA@LB@ \|\|\|\|\|:\|\|\|\|\|\|@LB@ GCUAAUGCACUU@LB@3'-AUU...UUUAG CAUUU...AUG-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -16.5289 kcal/mol@LB@Unfolding Energy - mRNA 2.50651 kcal/mol@LB@Unfolding Energy - sRNA 2.62518 kcal/mol@LB@@LB@Position - mRNA 49 -- 60@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 44 -- 50@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)

Job resubmission

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service.

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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