Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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	Additional homologs
3	7.57e-07	0.0008889	b1763	topB	-11.97	0.035059	233 -- 258	1 -- 37	DNA topoisomerase III		_____________232___________________________________259\n_____________\|_____________________________________\|\n5'-UCU...AGUCU_____________________________________CCAAA...GUA-3'\n______________GGCGC_GCG_CCAUUGCU_GAUGU________CCUGC\n______________:\|\|\|\|_:\|\|_\|\|\|\|:\|\|\|_\|\|:\|\|________\|\|\|\|\|\n______________UCGCG_UGC_GGUAGCGA_CUGCA________GGACG\n3'-UUU...AUACC_____U___G________A_____ACGUAAGU_____-5'\n_____________\|____________________________________\|\n_____________38___________________________________1\n	242 -- 248	20 -- 26	-35.9728 kcal/mol	8.72127 kcal/mol	15.288 kcal/mol	232 259@LB@ \| \|@LB@5'-UCU...AGUCU CCAAA...GUA-3'@LB@ GGCGC GCG CCAUUGCU GAUGU CCUGC@LB@ :\|\|\|\| :\|\| \|\|\|\|:\|\|\| \|\|:\|\| \|\|\|\|\|@LB@ UCGCG UGC GGUAGCGA CUGCA GGACG@LB@3'-UUU...AUACC U G A ACGUAAGU -5'@LB@ \| \|@LB@ 38 1@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -35.9728 kcal/mol@LB@Unfolding Energy - mRNA 8.72127 kcal/mol@LB@Unfolding Energy - sRNA 15.288 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 1 -- 37@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 20 -- 26@LB@
4	1.28e-06	0.001128	b0884	infA	-17.67	0.000535	178 -- 264	1 -- 71	translation initiation factor IF-1		_____________177_______________________________________________________________________________________265\n_____________\|_________________________________________________________________________________________\|\n5'-UUU...UUACG________ACCCC______UUAGAUGGCCAA_____________U__AA_____G__A___________AA______CUAA____A___UCCGC...CUG-3'\n______________GUAGUGAU_____AGAGGA____________AG_AAGACAAUAU_GA__UGCAA_GU_CCGUU_CUUGA__CGUUGC____UACC_UGU\n______________\|:\|\|\|:\|\|_____\|:\|\|\|\|____________\|\|_\|\|\|\|\|\|\|\|\|\|_\|\|__:\|\|\|\|_\|:_\|\|:\|:_\|\|\|\|\|__\|\|\|\|\|\|____:\|\|\|_\|\|:\n______________CGUCAUUA_____UUUCCU____________UC_UUCUGUUAUA_CU__GCGUU_CG_GGUAG_GAACU__GCAACG____GUGG_ACG\n3'-UUU...CGAUA________AGUUU____________________A__________C__C______G________C_____________UAA_________-5'\n_____________\|________________________________________________________________________________________\|\n_____________72_______________________________________________________________________________________1\n	214 -- 220	40 -- 46	-55.7119 kcal/mol	17.4656 kcal/mol	20.5786 kcal/mol	177 265@LB@ \| \|@LB@5'-UUU...UUACG ACCCC UUAGAUGGCCAA U AA G A AA CUAA A UCCGC...CUG-3'@LB@ GUAGUGAU AGAGGA AG AAGACAAUAU GA UGCAA GU CCGUU CUUGA CGUUGC UACC UGU@LB@ \|:\|\|\|:\|\| \|:\|\|\|\| \|\| \|\|\|\|\|\|\|\|\|\| \|\| :\|\|\|\| \|: \|\|:\|: \|\|\|\|\| \|\|\|\|\|\| :\|\|\| \|\|:@LB@ CGUCAUUA UUUCCU UC UUCUGUUAUA CU GCGUU CG GGUAG GAACU GCAACG GUGG ACG@LB@3'-UUU...CGAUA AGUUU A C C G C UAA -5'@LB@ \| \|@LB@ 72 1@LB@@LB@@LB@Energy -17.67 kcal/mol@LB@Hybridization Energy -55.7119 kcal/mol@LB@Unfolding Energy - mRNA 17.4656 kcal/mol@LB@Unfolding Energy - sRNA 20.5786 kcal/mol@LB@@LB@Position - mRNA 178 -- 264@LB@Position - sRNA 1 -- 71@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 40 -- 46@LB@
10	1.762e-05	0.005627	b1112	bhsA	-13.86	0.010205	165 -- 186	1 -- 22	biofilm cell surface and signaling protein	b0806 b0802	_____________164_____________________187\n_____________\|_______________________\|\n5'-UAA...UAAUU________AC_U___________AUAAG...AAC-3'\n______________GCUUG_CG__G_CAUUCAUCUGC\n______________\|\|\|\|\|_\|\|__\|_\|\|\|\|\|\|:\|\|\|\|\n______________CGAAC_GC__C_GUAAGUGGACG\n3'-UUU...GGUAG_____U__AA_____________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	180 -- 186	1 -- 7	-25.8922 kcal/mol	3.94114 kcal/mol	8.09964 kcal/mol	164 187@LB@ \| \|@LB@5'-UAA...UAAUU AC U AUAAG...AAC-3'@LB@ GCUUG CG G CAUUCAUCUGC@LB@ \|\|\|\|\| \|\| \| \|\|\|\|\|\|:\|\|\|\|@LB@ CGAAC GC C GUAAGUGGACG@LB@3'-UUU...GGUAG U AA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -25.8922 kcal/mol@LB@Unfolding Energy - mRNA 3.94114 kcal/mol@LB@Unfolding Energy - sRNA 8.09964 kcal/mol@LB@@LB@Position - mRNA 165 -- 186@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 1 -- 7@LB@
12	2.043e-05	0.005627	b3935	priA	-14.36	0.007166	198 -- 229	1 -- 34	Primosome factor n' (replication factor Y)		_____________197________________________________230\n_____________\|__________________________________\|\n5'-GAA...AUGAU__U___________CC________C______C__UCCGC...GCG-3'\n______________GC_AUGCCCGUUGC___ACGUUGC__UUGCC_GU\n______________\|\|_\|:\|\|\|\|:\|:\|\|___\|\|\|\|\|\|\|__\|::\|\|_\|:\n______________CG_UGCGGGUAGCG___UGCAACG__AGUGG_CG\n3'-UUU...CCUCG__U___________AAC_______UA_____A__-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	214 -- 220	11 -- 17	-36.548 kcal/mol	6.92453 kcal/mol	15.2664 kcal/mol	197 230@LB@ \| \|@LB@5'-GAA...AUGAU U CC C C UCCGC...GCG-3'@LB@ GC AUGCCCGUUGC ACGUUGC UUGCC GU@LB@ \|\| \|:\|\|\|\|:\|:\|\| \|\|\|\|\|\|\| \|::\|\| \|:@LB@ CG UGCGGGUAGCG UGCAACG AGUGG CG@LB@3'-UUU...CCUCG U AAC UA A -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -36.548 kcal/mol@LB@Unfolding Energy - mRNA 6.92453 kcal/mol@LB@Unfolding Energy - sRNA 15.2664 kcal/mol@LB@@LB@Position - mRNA 198 -- 229@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 11 -- 17@LB@
13	2.167e-05	0.005627	b0123	cueO	-18.83	0.000188	100 -- 180	1 -- 93	multicopper oxidase (laccase)		_____________99__________________________________________________________________________________________________181\n_____________\|___________________________________________________________________________________________________\|\n5'-CUG...CAUUA________UUA________C______CU___CC___CCGU_______________U___________________A________U______________UUAAG...CGU-3'\n______________UUGU_CGA___AAUUGUGU__UGCGG__UGA__UUC____AAGGGGAAG___GAC_____________AUGCUCA_CGUUUGAU_UUGU_UUCGCCUGC\n______________\|:\|\|_\|\|\|___\|\|\|\|\|\|\|:__\|\|\|:\|__\|:\|__\|\|\|____\|\|::\|\|\|\|\|___\|\|\|_____________\|:\|\|:\|\|_\|\|:\|\|\|\|:_\|\|\|:_\|\|\|:\|\|\|\|\|\n______________AGCA_GCU___UUAACACG__ACGUC__AUU__AAG____UUUUCCUUC___CUG_____________UGCGGGU_GCGAACUG_AACG_AAGUGGACG\n3'-UUU...GCCGC____U___UAG________AU_______________UU___________AUU___UUAUACCUCGCGU_______A________C____U_________-5'\n_____________\|__________________________________________________________________________________________________\|\n_____________94_________________________________________________________________________________________________1\n	174 -- 180	1 -- 7	-64.9216 kcal/mol	25.1682 kcal/mol	20.925 kcal/mol	99 181@LB@ \| \|@LB@5'-CUG...CAUUA UUA C CU CC CCGU U A U UUAAG...CGU-3'@LB@ UUGU CGA AAUUGUGU UGCGG UGA UUC AAGGGGAAG GAC AUGCUCA CGUUUGAU UUGU UUCGCCUGC@LB@ \|:\|\| \|\|\| \|\|\|\|\|\|\|: \|\|\|:\| \|:\| \|\|\| \|\|::\|\|\|\|\| \|\|\| \|:\|\|:\|\| \|\|:\|\|\|\|: \|\|\|: \|\|\|:\|\|\|\|\|@LB@ AGCA GCU UUAACACG ACGUC AUU AAG UUUUCCUUC CUG UGCGGGU GCGAACUG AACG AAGUGGACG@LB@3'-UUU...GCCGC U UAG AU UU AUU UUAUACCUCGCGU A C U -5'@LB@ \| \|@LB@ 94 1@LB@@LB@@LB@Energy -18.83 kcal/mol@LB@Hybridization Energy -64.9216 kcal/mol@LB@Unfolding Energy - mRNA 25.1682 kcal/mol@LB@Unfolding Energy - sRNA 20.925 kcal/mol@LB@@LB@Position - mRNA 100 -- 180@LB@Position - sRNA 1 -- 93@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 1 -- 7@LB@
16	3.593e-05	0.007912	b2294	yfbU	-10.97	0.063921	276 -- 297	1 -- 22	UPF0304 family protein		_____________275____________________298\n_____________\|______________________\|\n5'-GCA...CAAAU___GA_____ACCG________AAA-3'\n______________GCU__ACGUU____UCGCCUGC\n______________\|\|\|__\|\|\|\|\|____\|\|:\|\|\|\|\|\n______________CGA__UGCAA____AGUGGACG\n3'-UUU...GGUAG___AC_____CGUA________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	291 -- 297	1 -- 7	-25.1893 kcal/mol	6.12655 kcal/mol	8.09964 kcal/mol	275 298@LB@ \| \|@LB@5'-GCA...CAAAU GA ACCG AAA-3'@LB@ GCU ACGUU UCGCCUGC@LB@ \|\|\| \|\|\|\|\| \|\|:\|\|\|\|\|@LB@ CGA UGCAA AGUGGACG@LB@3'-UUU...GGUAG AC CGUA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.97 kcal/mol@LB@Hybridization Energy -25.1893 kcal/mol@LB@Unfolding Energy - mRNA 6.12655 kcal/mol@LB@Unfolding Energy - sRNA 8.09964 kcal/mol@LB@@LB@Position - mRNA 276 -- 297@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 1 -- 7@LB@
22	6.552e-05	0.01049	b3829	metE	-13.68	0.011485	203 -- 246	1 -- 47	5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase		_____________202_____________________________________________247\n_____________\|_______________________________________________\|\n5'-GAG...AAAAU________U__AUC____A_______G__UCCCUC_____G______GUCGC...GUG-3'\n______________GACAAUAU_GA_____AC_CCC_UCG_UU______GCGUU_GCCUGC\n______________\|\|\|\|\|\|\|\|_\|\|_____\|\|_\|\|\|_\|\|\|_\|\|______\|\|:\|\|_:\|\|\|\|\|\n______________CUGUUAUA_CU_____UG_GGG_AGC_AA______CGUAA_UGGACG\n3'-UUU...UCAUU________C__CGCGU__C___U___G__CUGCAA_____G______-5'\n_____________\|______________________________________________\|\n_____________48_____________________________________________1\n	204 -- 210	40 -- 46	-38.0501 kcal/mol	7.59426 kcal/mol	16.7767 kcal/mol	202 247@LB@ \| \|@LB@5'-GAG...AAAAU U AUC A G UCCCUC G GUCGC...GUG-3'@LB@ GACAAUAU GA AC CCC UCG UU GCGUU GCCUGC@LB@ \|\|\|\|\|\|\|\| \|\| \|\| \|\|\| \|\|\| \|\| \|\|:\|\| :\|\|\|\|\|@LB@ CUGUUAUA CU UG GGG AGC AA CGUAA UGGACG@LB@3'-UUU...UCAUU C CGCGU C U G CUGCAA G -5'@LB@ \| \|@LB@ 48 1@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -38.0501 kcal/mol@LB@Unfolding Energy - mRNA 7.59426 kcal/mol@LB@Unfolding Energy - sRNA 16.7767 kcal/mol@LB@@LB@Position - mRNA 203 -- 246@LB@Position - sRNA 1 -- 47@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 40 -- 46@LB@
32	0.0001844	0.0203	b0006	yaaA	-10.88	0.067423	215 -- 223	1 -- 9	peroxide resistance protein lowers intracellular iron		_____________214_______224\n_____________\|_________\|\n5'-UUC...CUUAU_________GAAAA...AGU-3'\n______________UUCACCUGC\n______________\|\|\|\|\|\|\|\|\|\n______________AAGUGGACG\n3'-UUU...AACGU_________-5'\n_____________\|________\|\n_____________10_______1\n	217 -- 223	1 -- 7	-15.2887 kcal/mol	2.04449 kcal/mol	2.37317 kcal/mol	214 224@LB@ \| \|@LB@5'-UUC...CUUAU GAAAA...AGU-3'@LB@ UUCACCUGC@LB@ \|\|\|\|\|\|\|\|\|@LB@ AAGUGGACG@LB@3'-UUU...AACGU -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -10.88 kcal/mol@LB@Hybridization Energy -15.2887 kcal/mol@LB@Unfolding Energy - mRNA 2.04449 kcal/mol@LB@Unfolding Energy - sRNA 2.37317 kcal/mol@LB@@LB@Position - mRNA 215 -- 223@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 1 -- 7@LB@
34	0.0002646	0.02697	b1206	dauA	-13.80	0.010599	120 -- 158	1 -- 34	C4-dicarboxylic acid transporter		_____________119_____________________________________159\n_____________\|_______________________________________\|\n5'-CCU...UGUCU_____A____U____A____CUA___CUCC_________CAUUU...UGA-3'\n______________GUAAU_UCCA_UUGU_UGAC___UGC____UUCACCUGC\n______________\|:\|\|:_:\|\|\|_\|:\|:_\|\|\|\|___\|\|\|____\|\|\|\|\|\|\|\|\|\n______________CGUUG_GGGU_AGCG_ACUG___ACG____AAGUGGACG\n3'-UUU...CCUCG_____C_________A____CA____U____________-5'\n_____________\|______________________________________\|\n_____________35_____________________________________1\n	152 -- 158	1 -- 7	-32.3364 kcal/mol	3.2737 kcal/mol	15.2664 kcal/mol	119 159@LB@ \| \|@LB@5'-CCU...UGUCU A U A CUA CUCC CAUUU...UGA-3'@LB@ GUAAU UCCA UUGU UGAC UGC UUCACCUGC@LB@ \|:\|\|: :\|\|\| \|:\|: \|\|\|\| \|\|\| \|\|\|\|\|\|\|\|\|@LB@ CGUUG GGGU AGCG ACUG ACG AAGUGGACG@LB@3'-UUU...CCUCG C A CA U -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -32.3364 kcal/mol@LB@Unfolding Energy - mRNA 3.2737 kcal/mol@LB@Unfolding Energy - sRNA 15.2664 kcal/mol@LB@@LB@Position - mRNA 120 -- 158@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 1 -- 7@LB@
47	0.0004845	0.03632	b0102	zapD	-14.30	0.007459	100 -- 148	1 -- 47	FtsZ stabilizer		_____________99____________________________________________________149\n_____________\|_____________________________________________________\|\n5'-ACC...UCAUU_______AC_______CCGG___________AUCG________C_________ACGCA...CCA-3'\n______________GAUAAUA___GGCGCA____AUG_CUAUCGC____GAUGUUGC___CGCCUGC\n______________\|\|:\|\|\|\|___:\|\|\|\|\|____\|:\|_\|:\|\|\|\|\|____\|\|:\|\|\|\|\|___\|:\|\|\|\|\|\n______________CUGUUAU___UCGCGU____UGC_GGUAGCG____CUGCAACG___GUGGACG\n3'-UUU...UCAUU_______ACC_____________G_______AA__________UAA_______-5'\n_____________\|____________________________________________________\|\n_____________48___________________________________________________1\n	142 -- 148	1 -- 7	-50.0565 kcal/mol	18.9794 kcal/mol	16.7767 kcal/mol	99 149@LB@ \| \|@LB@5'-ACC...UCAUU AC CCGG AUCG C ACGCA...CCA-3'@LB@ GAUAAUA GGCGCA AUG CUAUCGC GAUGUUGC CGCCUGC@LB@ \|\|:\|\|\|\| :\|\|\|\|\| \|:\| \|:\|\|\|\|\| \|\|:\|\|\|\|\| \|:\|\|\|\|\|@LB@ CUGUUAU UCGCGU UGC GGUAGCG CUGCAACG GUGGACG@LB@3'-UUU...UCAUU ACC G AA UAA -5'@LB@ \| \|@LB@ 48 1@LB@@LB@@LB@Energy -14.30 kcal/mol@LB@Hybridization Energy -50.0565 kcal/mol@LB@Unfolding Energy - mRNA 18.9794 kcal/mol@LB@Unfolding Energy - sRNA 16.7767 kcal/mol@LB@@LB@Position - mRNA 100 -- 148@LB@Position - sRNA 1 -- 47@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 1 -- 7@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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usability assessment

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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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