Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
65	0.00343	0.1851	b4363	yjjB	-10.89	0.196296	181 -- 193	20 -- 32	DUF3815 family inner membrane protein		_____________180___________194\n_____________\|_____________\|\n5'-ACU...CACUG____UU_______UACGC...GGG-3'\n______________ACGA__UGGGGGC\n______________\|\|:\|__\|\|\|\|\|:\|\n______________UGUU__ACCCCUG\n3'-UUU...CGAGG____UU_______UAGUU...CCG-5'\n_____________\|_____________\|\n_____________33____________19\n	187 -- 193	20 -- 26	-17.0561 kcal/mol	4.01516 kcal/mol	2.14699 kcal/mol	180 194@LB@ \| \|@LB@5'-ACU...CACUG UU UACGC...GGG-3'@LB@ ACGA UGGGGGC@LB@ \|\|:\| \|\|\|\|\|:\|@LB@ UGUU ACCCCUG@LB@3'-UUU...CGAGG UU UAGUU...CCG-5'@LB@ \| \|@LB@ 33 19@LB@@LB@@LB@Energy -10.89 kcal/mol@LB@Hybridization Energy -17.0561 kcal/mol@LB@Unfolding Energy - mRNA 4.01516 kcal/mol@LB@Unfolding Energy - sRNA 2.14699 kcal/mol@LB@@LB@Position - mRNA 181 -- 193@LB@Position - sRNA 20 -- 32@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 20 -- 26@LB@
100	0.006296	0.2188	b1321	ycjX	-13.69	0.055797	38 -- 45	18 -- 25	DUF463 family protein puatative P-loop NTPase		_____________37_______46\n_____________\|________\|\n5'-UGA...UAGUA________AGGUC...CAG-3'\n______________GGGGACAU\n______________\|\|\|\|\|\|\|\|\n______________CCCCUGUA\n3'-UUU...UUUUA________GUUUC...CCG-5'\n_____________\|________\|\n_____________26_______17\n	39 -- 45	18 -- 24	-15.5505 kcal/mol	1.21152 kcal/mol	0.65218 kcal/mol	37 46@LB@ \| \|@LB@5'-UGA...UAGUA AGGUC...CAG-3'@LB@ GGGGACAU@LB@ \|\|\|\|\|\|\|\|@LB@ CCCCUGUA@LB@3'-UUU...UUUUA GUUUC...CCG-5'@LB@ \| \|@LB@ 26 17@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -15.5505 kcal/mol@LB@Unfolding Energy - mRNA 1.21152 kcal/mol@LB@Unfolding Energy - sRNA 0.65218 kcal/mol@LB@@LB@Position - mRNA 38 -- 45@LB@Position - sRNA 18 -- 25@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 18 -- 24@LB@
106	0.007048	0.2333	b4512	ybdD	-9.12	0.369799	33 -- 54	1 -- 25	DUF466 family protein	b4353	_____________32________________________55\n_____________\|_________________________\|\n5'-GCA...GAGGG___________C___U_________UUAGU...GGG-3'\n______________GGGGAUGUUGG_GAA__GU__UGGC\n______________\|\|\|\|\|::\|:::_\|\|\|__\|:__\|\|\|\|\n______________CCCCUGUAGUU_CUU__CG__ACCG\n3'-UUU...UUUUA___________U___UU__UC____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	36 -- 42	16 -- 22	-21.5624 kcal/mol	9.92515 kcal/mol	2.51748 kcal/mol	32 55@LB@ \| \|@LB@5'-GCA...GAGGG C U UUAGU...GGG-3'@LB@ GGGGAUGUUGG GAA GU UGGC@LB@ \|\|\|\|\|::\|::: \|\|\| \|: \|\|\|\|@LB@ CCCCUGUAGUU CUU CG ACCG@LB@3'-UUU...UUUUA U UU UC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -21.5624 kcal/mol@LB@Unfolding Energy - mRNA 9.92515 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 33 -- 54@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 16 -- 22@LB@
142	0.01047	0.2504	b3998	nfi	-11.68	0.142276	34 -- 51	5 -- 21	endonuclease V; deoxyinosine 3' endonuclease		_____________33_________________52\n_____________\|__________________\|\n5'-UGG...UGCCC_________A________CGACU...GAG-3'\n______________GCAUUGAAG_AGAAGUAG\n______________:\|\|\|::\|\|\|_\|:\|\|\|:\|\|\n______________UGUAGUUUC_UUUUCGUC\n3'-UUU...ACCCC__________________ACCG-5'\n_____________\|__________________\|\n_____________22_________________4\n	45 -- 51	5 -- 11	-17.0993 kcal/mol	3.91468 kcal/mol	1.5073 kcal/mol	33 52@LB@ \| \|@LB@5'-UGG...UGCCC A CGACU...GAG-3'@LB@ GCAUUGAAG AGAAGUAG@LB@ :\|\|\|::\|\|\| \|:\|\|\|:\|\|@LB@ UGUAGUUUC UUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -17.0993 kcal/mol@LB@Unfolding Energy - mRNA 3.91468 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 34 -- 51@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 5 -- 11@LB@
102	0.006464	0.2224	b3785	wzzE	-10.51	0.228012	146 -- 168	1 -- 22	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein		_____________145_____________________169\n_____________\|_______________________\|\n5'-GCU...ACGCA___UG__U_____UC________AGCCC...UUA-3'\n______________GAC__CG_AGAAA__GUGGUGGC\n______________\|\|\|__\|:_\|\|\|\|\|__\|::\|\|\|\|\|\n______________CUG__GU_UCUUU__CGUCACCG\n3'-UUU...UACCC___UA__U_____U_________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	162 -- 168	1 -- 7	-19.8866 kcal/mol	7.83936 kcal/mol	1.54023 kcal/mol	145 169@LB@ \| \|@LB@5'-GCU...ACGCA UG U UC AGCCC...UUA-3'@LB@ GAC CG AGAAA GUGGUGGC@LB@ \|\|\| \|: \|\|\|\|\| \|::\|\|\|\|\|@LB@ CUG GU UCUUU CGUCACCG@LB@3'-UUU...UACCC UA U U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -19.8866 kcal/mol@LB@Unfolding Energy - mRNA 7.83936 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 146 -- 168@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 1 -- 7@LB@
37	0.001785	0.1648	b3933	ftsN	-15.64	0.019200	24 -- 52	1 -- 29	essential cell division protein		_____________23______________________________53\n_____________\|_______________________________\|\n5'-AGC...UGAUC_____CA______A__CGUU___________UCUCG...CUC-3'\n______________AAAUG__GGGGCA_CA______GGCAGUGGC\n______________\|\|\|\|\|__\|\|\|:\|\|_\|\|______:\|\|\|\|\|\|\|\|\n______________UUUAC__CCCUGU_GU______UCGUCACCG\n3'-UUU...GGUGU_____________A__UUCUUU_________-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	46 -- 52	1 -- 7	-29.0551 kcal/mol	10.8938 kcal/mol	2.51907 kcal/mol	23 53@LB@ \| \|@LB@5'-AGC...UGAUC CA A CGUU UCUCG...CUC-3'@LB@ AAAUG GGGGCA CA GGCAGUGGC@LB@ \|\|\|\|\| \|\|\|:\|\| \|\| :\|\|\|\|\|\|\|\|@LB@ UUUAC CCCUGU GU UCGUCACCG@LB@3'-UUU...GGUGU A UUCUUU -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.64 kcal/mol@LB@Hybridization Energy -29.0551 kcal/mol@LB@Unfolding Energy - mRNA 10.8938 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 24 -- 52@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 1 -- 7@LB@
146	0.01079	0.2504	b2453	eutG	-16.22	0.013596	18 -- 37	1 -- 22	ethanol dehydrogenase involved in ethanolamine utilization; aldehyde reductase		_____________17_____________________38\n_____________\|______________________\|\n5'-GGC...CGCCC_____AUU______________AUUAC...GUC-3'\n______________GGCAU____GAAGGGCAG_GGC\n______________\|:\|\|\|____\|\|\|::\|\|\|\|_\|\|\|\n______________CUGUA____CUUUUCGUC_CCG\n3'-UUU...UACCC_____GUUU_________A___-5'\n_____________\|_____________________\|\n_____________23____________________1\n	28 -- 34	5 -- 11	-23.1742 kcal/mol	5.41796 kcal/mol	1.54023 kcal/mol	17 38@LB@ \| \|@LB@5'-GGC...CGCCC AUU AUUAC...GUC-3'@LB@ GGCAU GAAGGGCAG GGC@LB@ \|:\|\|\| \|\|\|::\|\|\|\| \|\|\|@LB@ CUGUA CUUUUCGUC CCG@LB@3'-UUU...UACCC GUUU A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -23.1742 kcal/mol@LB@Unfolding Energy - mRNA 5.41796 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 18 -- 37@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 5 -- 11@LB@
80	0.004856	0.213	b1478	adhP	-8.37	0.463200	263 -- 276	48 -- 59	ethanol-active dehydrogenase/acetaldehyde-active reductase		_____________262____________277\n_____________\|______________\|\n5'-GCA...CGCUC_______CA_____AAGCC...GUU-3'\n______________ACUGAAA__UGGCG\n______________\|\|:\|\|\|\|__\|\|\|\|\|\n______________UGGCUUU__ACCGC\n3'-UUU...GAACU______________CCCAA...CCG-5'\n_____________\|______________\|\n_____________60_____________47\n	263 -- 269	53 -- 59	-14.4135 kcal/mol	2.08604 kcal/mol	3.96136 kcal/mol	262 277@LB@ \| \|@LB@5'-GCA...CGCUC CA AAGCC...GUU-3'@LB@ ACUGAAA UGGCG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ UGGCUUU ACCGC@LB@3'-UUU...GAACU CCCAA...CCG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -14.4135 kcal/mol@LB@Unfolding Energy - mRNA 2.08604 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 263 -- 276@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 53 -- 59@LB@
26	0.001009	0.1361	b3731	atpC	-14.21	0.042680	144 -- 160	2 -- 20	F1 sector of membrane-bound ATP synthase epsilon subunit		_____________143_________________161\n_____________\|___________________\|\n5'-UCC...GGUUC______________U____AAAAA...UGG-3'\n______________CAUCGAAGA__AGC_GUGG\n______________\|\|\|\|:\|\|\|\|__\|\|\|_\|\|\|\|\n______________GUAGUUUCU__UCG_CACC\n3'-UUU...CCCCU_________UU___U____G-5'\n_____________\|___________________\|\n_____________21__________________1\n	146 -- 152	12 -- 18	-19.7705 kcal/mol	4.1055 kcal/mol	1.45839 kcal/mol	143 161@LB@ \| \|@LB@5'-UCC...GGUUC U AAAAA...UGG-3'@LB@ CAUCGAAGA AGC GUGG@LB@ \|\|\|\|:\|\|\|\| \|\|\| \|\|\|\|@LB@ GUAGUUUCU UCG CACC@LB@3'-UUU...CCCCU UU U G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -14.21 kcal/mol@LB@Hybridization Energy -19.7705 kcal/mol@LB@Unfolding Energy - mRNA 4.1055 kcal/mol@LB@Unfolding Energy - sRNA 1.45839 kcal/mol@LB@@LB@Position - mRNA 144 -- 160@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 12 -- 18@LB@
25	0.0009834	0.1361	b3733	atpG	-13.27	0.068654	183 -- 205	1 -- 22	F1 sector of membrane-bound ATP synthase gamma subunit		_____________182_____________________206\n_____________\|_______________________\|\n5'-GGC...CGCAA________________UCA____CGGCG...GUA-3'\n______________GGCAUUGAGGAGAAGC___UGGC\n______________\|:\|\|\|::\|:\|\|:\|\|\|\|___\|\|\|\|\n______________CUGUAGUUUCUUUUCG___ACCG\n3'-UUU...UACCC________________UC_____-5'\n_____________\|______________________\|\n_____________23_____________________1\n	192 -- 198	7 -- 13	-25.5897 kcal/mol	10.7799 kcal/mol	1.54023 kcal/mol	182 206@LB@ \| \|@LB@5'-GGC...CGCAA UCA CGGCG...GUA-3'@LB@ GGCAUUGAGGAGAAGC UGGC@LB@ \|:\|\|\|::\|:\|\|:\|\|\|\| \|\|\|\|@LB@ CUGUAGUUUCUUUUCG ACCG@LB@3'-UUU...UACCC UC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -13.27 kcal/mol@LB@Hybridization Energy -25.5897 kcal/mol@LB@Unfolding Energy - mRNA 10.7799 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@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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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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