Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
57	0.005155	0.3024	b3091	uxaA	-13.05	0.035558	147 -- 159	6 -- 19	altronate hydrolase		_____________146____________160\n_____________\|______________\|\n5'-CUG...UGCUU______________GACUA...CGC-3'\n______________UAAC_AAUGCGCGU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AUUG_UUACGCGCA\n3'-UUU...CUACU____U_________GAAAG-5'\n_____________\|______________\|\n_____________20_____________5\n	153 -- 159	6 -- 12	-17.3524 kcal/mol	3.0727 kcal/mol	1.22941 kcal/mol	146 160@LB@ \| \|@LB@5'-CUG...UGCUU GACUA...CGC-3'@LB@ UAAC AAUGCGCGU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ AUUG UUACGCGCA@LB@3'-UUU...CUACU U GAAAG-5'@LB@ \| \|@LB@ 20 5@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -17.3524 kcal/mol@LB@Unfolding Energy - mRNA 3.0727 kcal/mol@LB@Unfolding Energy - sRNA 1.22941 kcal/mol@LB@@LB@Position - mRNA 147 -- 159@LB@Position - sRNA 6 -- 19@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 6 -- 12@LB@
184	0.01824	0.3104	b2055	wcaE	-6.17	0.461247	221 -- 230	4 -- 12	putative glycosyl transferase		_____________220________231\n_____________\|__________\|\n5'-ACU...AUCAC__U_______CGUAA...GCU-3'\n______________UG_CGCGUUU\n______________\|\|_\|\|\|\|\|:\|\n______________AC_GCGCAGA\n3'-UUU...UGUUU__________AAG-5'\n_____________\|__________\|\n_____________13_________3\n	224 -- 230	4 -- 10	-10.1102 kcal/mol	2.78254 kcal/mol	1.16019 kcal/mol	220 231@LB@ \| \|@LB@5'-ACU...AUCAC U CGUAA...GCU-3'@LB@ UG CGCGUUU@LB@ \|\| \|\|\|\|\|:\|@LB@ AC GCGCAGA@LB@3'-UUU...UGUUU AAG-5'@LB@ \| \|@LB@ 13 3@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -10.1102 kcal/mol@LB@Unfolding Energy - mRNA 2.78254 kcal/mol@LB@Unfolding Energy - sRNA 1.16019 kcal/mol@LB@@LB@Position - mRNA 221 -- 230@LB@Position - sRNA 4 -- 12@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 4 -- 10@LB@
29	0.001844	0.2094	b2047	wcaJ	-13.26	0.032615	200 -- 222	7 -- 21	colanic biosynthesis UDP-glucose lipid carrier transferase		_____________199_____________________223\n_____________\|_______________________\|\n5'-GCA...ACAAC__________CUAAAAAA_____AGCGA...UAU-3'\n______________GAUGACAAAU________GCGCG\n______________\|\|\|:\|\|\|\|\|\|________\|\|\|\|\|\n______________CUAUUGUUUA________CGCGC\n3'-UUU...UACUA_______________________AGAAAG-5'\n_____________\|_______________________\|\n_____________22______________________6\n	203 -- 209	12 -- 18	-17.5174 kcal/mol	3.01646 kcal/mol	1.24179 kcal/mol	199 223@LB@ \| \|@LB@5'-GCA...ACAAC CUAAAAAA AGCGA...UAU-3'@LB@ GAUGACAAAU GCGCG@LB@ \|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUUUA CGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -17.5174 kcal/mol@LB@Unfolding Energy - mRNA 3.01646 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 200 -- 222@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 12 -- 18@LB@
53	0.004896	0.3024	b3790	wecD	-9.15	0.167607	125 -- 139	7 -- 21	TDP-fucosamine acetyltransferase		_____________124_____________140\n_____________\|_______________\|\n5'-CUG...GGCUC_________G_____AAGCG...UGA-3'\n______________GAUGACGAG_GUGUG\n______________\|\|\|:\|\|:\|:_\|:\|:\|\n______________CUAUUGUUU_CGCGC\n3'-UUU...UACUA_________A_____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	126 -- 132	14 -- 20	-15.9636 kcal/mol	5.57309 kcal/mol	1.24179 kcal/mol	124 140@LB@ \| \|@LB@5'-CUG...GGCUC G AAGCG...UGA-3'@LB@ GAUGACGAG GUGUG@LB@ \|\|\|:\|\|:\|: \|:\|:\|@LB@ CUAUUGUUU CGCGC@LB@3'-UUU...UACUA A AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -15.9636 kcal/mol@LB@Unfolding Energy - mRNA 5.57309 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 125 -- 139@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 14 -- 20@LB@
105	0.01074	0.3104	b3791	wecE	-13.91	0.024834	1 -- 12	7 -- 18	TDP-4-oxo-6-deoxy-D-glucose transaminase		______________1___________13\n______________\|___________\|\n___________5'-____________AAUUG...CCC-3'\n______________GACAGAUGCGCG\n______________:\|\|\|:\|\|\|\|\|\|\|\n______________UUGUUUACGCGC\n3'-UUU...UACUA____________AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	6 -- 12	7 -- 13	-19.4696 kcal/mol	4.34626 kcal/mol	1.20891 kcal/mol	1 13@LB@ \| \|@LB@ 5'- AAUUG...CCC-3'@LB@ GACAGAUGCGCG@LB@ :\|\|\|:\|\|\|\|\|\|\|@LB@ UUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -13.91 kcal/mol@LB@Hybridization Energy -19.4696 kcal/mol@LB@Unfolding Energy - mRNA 4.34626 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 7 -- 13@LB@
60	0.00555	0.3084	b2062	wza	-10.85	0.086669	18 -- 25	4 -- 11	colanic acid export protein; outer membrane auxillary lipoprotein		_____________17_______26\n_____________\|________\|\n5'-AAA...CGGUA________GGAUG...GCA-3'\n______________GCGUGUCU\n______________\|\|\|:\|\|\|\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	19 -- 25	4 -- 10	-13.9362 kcal/mol	1.92535 kcal/mol	1.15639 kcal/mol	17 26@LB@ \| \|@LB@5'-AAA...CGGUA GGAUG...GCA-3'@LB@ GCGUGUCU@LB@ \|\|\|:\|\|\|\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -13.9362 kcal/mol@LB@Unfolding Energy - mRNA 1.92535 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 18 -- 25@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 4 -- 10@LB@
66	0.006019	0.3087	b0223	yafJ	-7.05	0.351504	68 -- 78	1 -- 10	type 2 glutamine amidotransferase family protein		_____________67__________79\n_____________\|___________\|\n5'-GCG...GCUGA________A__AUGCC...AAG-3'\n______________CGCGUCUU_UC\n______________\|\|\|\|\|\|\|\|_\|\|\n______________GCGCAGAA_AG\n3'-UUU...UUUAC___________-5'\n_____________\|__________\|\n_____________11_________1\n	69 -- 75	3 -- 9	-12.9748 kcal/mol	4.76165 kcal/mol	1.16635 kcal/mol	67 79@LB@ \| \|@LB@5'-GCG...GCUGA A AUGCC...AAG-3'@LB@ CGCGUCUU UC@LB@ \|\|\|\|\|\|\|\| \|\|@LB@ GCGCAGAA AG@LB@3'-UUU...UUUAC -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -7.05 kcal/mol@LB@Hybridization Energy -12.9748 kcal/mol@LB@Unfolding Energy - mRNA 4.76165 kcal/mol@LB@Unfolding Energy - sRNA 1.16635 kcal/mol@LB@@LB@Position - mRNA 68 -- 78@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 3 -- 9@LB@
152	0.01445	0.3104	b0385	yaiC	-12.21	0.050169	39 -- 67	12 -- 42	diguanylate cyclase cellulose regualtor		_____________38_______________________________68\n_____________\|________________________________\|\n5'-CAA...CAACA_______________U______C_________UUAUG...CCG-3'\n______________AUCUCUGAA___AGG_GAUGAU_GUAAUAAGU\n______________\|\|\|\|\|\|\|\|\|___\|\|\|_\|\|\|\|\|\|_:\|\|\|:\|\|:\|\n______________UAGAGACUU___UCC_CUACUA_UAUUGUUUA\n3'-UUU...UAAAG_________AAG__________C_________CGCGC...AAG-5'\n_____________\|________________________________\|\n_____________43_______________________________11\n	40 -- 46	35 -- 41	-28.8147 kcal/mol	7.19368 kcal/mol	9.40905 kcal/mol	38 68@LB@ \| \|@LB@5'-CAA...CAACA U C UUAUG...CCG-3'@LB@ AUCUCUGAA AGG GAUGAU GUAAUAAGU@LB@ \|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\| :\|\|\|:\|\|:\|@LB@ UAGAGACUU UCC CUACUA UAUUGUUUA@LB@3'-UUU...UAAAG AAG C CGCGC...AAG-5'@LB@ \| \|@LB@ 43 11@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -28.8147 kcal/mol@LB@Unfolding Energy - mRNA 7.19368 kcal/mol@LB@Unfolding Energy - sRNA 9.40905 kcal/mol@LB@@LB@Position - mRNA 39 -- 67@LB@Position - sRNA 12 -- 42@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 35 -- 41@LB@
81	0.007385	0.3087	b0736	ybgC	-11.71	0.061637	220 -- 237	4 -- 21	acyl-CoA thioester hydrolase		_____________219________________238\n_____________\|__________________\|\n5'-UUG...GUUUC______C___U_______ACUAU...AAA-3'\n______________GAUGGC_GGU_CGCGUCU\n______________\|\|\|::\|_::\|_\|\|\|\|\|\|\|\n______________CUAUUG_UUA_GCGCAGA\n3'-UUU...UACUA______U___C_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	231 -- 237	4 -- 10	-19.027 kcal/mol	6.06673 kcal/mol	1.2552 kcal/mol	219 238@LB@ \| \|@LB@5'-UUG...GUUUC C U ACUAU...AAA-3'@LB@ GAUGGC GGU CGCGUCU@LB@ \|\|\|::\| ::\| \|\|\|\|\|\|\|@LB@ CUAUUG UUA GCGCAGA@LB@3'-UUU...UACUA U C AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -19.027 kcal/mol@LB@Unfolding Energy - mRNA 6.06673 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 220 -- 237@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 4 -- 10@LB@
67	0.006163	0.3087	b0773	ybhB	-10.36	0.105479	214 -- 228	7 -- 20	kinase inhibitor homolog UPF0098 family	b0545	_____________213_____________229\n_____________\|_______________\|\n5'-UGU...CAUCA_______UC______AUGGC...AUC-3'\n______________GUAACGA__UGCGCG\n______________:\|\|\|\|:\|__\|\|\|\|\|\|\n______________UAUUGUU__ACGCGC\n3'-UUU...ACUAC_______U_______AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	214 -- 220	14 -- 20	-16.0436 kcal/mol	4.44842 kcal/mol	1.23906 kcal/mol	213 229@LB@ \| \|@LB@5'-UGU...CAUCA UC AUGGC...AUC-3'@LB@ GUAACGA UGCGCG@LB@ :\|\|\|\|:\| \|\|\|\|\|\|@LB@ UAUUGUU ACGCGC@LB@3'-UUU...ACUAC U AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.0436 kcal/mol@LB@Unfolding Energy - mRNA 4.44842 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 214 -- 228@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 14 -- 20@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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