Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
93	0.005014	0.1855	b0091	murC	-15.25	0.013117	8 -- 30	73 -- 94	UDP-N-acetylmuramate:L-alanine ligase	_____________7_______________________31\n_____________\|_______________________\|\n____5'-CAGCUUA____________U__________CUGGC...GCG-3'\n______________GCGUGGAUGCUG_CGCCAACACC\n______________\|\|\|:\|:\|\|:\|\|\|_\|\|\|\|\|\|\|\|\|\|\n______________CGCGCUUAUGAC_GCGGUUGUGG\n3'-UUU...CCCCA_______________________UCCCU...GUG-5'\n_____________\|_______________________\|\n_____________95______________________72\n	24 -- 30	73 -- 79	-39.1057 kcal/mol	11.3 kcal/mol	12.5321 kcal/mol	7 31@LB@ \| \|@LB@ 5'-CAGCUUA U CUGGC...GCG-3'@LB@ GCGUGGAUGCUG CGCCAACACC@LB@ \|\|\|:\|:\|\|:\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ CGCGCUUAUGAC GCGGUUGUGG@LB@3'-UUU...CCCCA UCCCU...GUG-5'@LB@ \| \|@LB@ 95 72@LB@@LB@@LB@Energy -15.25 kcal/mol@LB@Hybridization Energy -39.1057 kcal/mol@LB@Unfolding Energy - mRNA 11.3 kcal/mol@LB@Unfolding Energy - sRNA 12.5321 kcal/mol@LB@@LB@Position - mRNA 8 -- 30@LB@Position - sRNA 73 -- 94@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 73 -- 79@LB@
114	0.006011	0.1855	b0422	xseB	-10.73	0.101337	104 -- 119	73 -- 87	exonuclease VII small subunit	_____________103______________120\n_____________\|________________\|\n5'-CAA...CGCUU________A__U____UUACC...AAG-3'\n______________UGCUGUGC_CA_CACC\n______________\|:\|\|\|:\|\|_\|\|_\|\|\|\|\n______________AUGACGCG_GU_GUGG\n3'-UUU...CGCUU___________U____UCCCU...GUG-5'\n_____________\|________________\|\n_____________88_______________72\n	105 -- 111	80 -- 86	-20.3088 kcal/mol	2.628 kcal/mol	6.95602 kcal/mol	103 120@LB@ \| \|@LB@5'-CAA...CGCUU A U UUACC...AAG-3'@LB@ UGCUGUGC CA CACC@LB@ \|:\|\|\|:\|\| \|\| \|\|\|\|@LB@ AUGACGCG GU GUGG@LB@3'-UUU...CGCUU U UCCCU...GUG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -10.73 kcal/mol@LB@Hybridization Energy -20.3088 kcal/mol@LB@Unfolding Energy - mRNA 2.628 kcal/mol@LB@Unfolding Energy - sRNA 6.95602 kcal/mol@LB@@LB@Position - mRNA 104 -- 119@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 80 -- 86@LB@
137	0.007754	0.1993	b4024	lysC	-8.53	0.257132	131 -- 141	73 -- 85	lysine-sensitive aspartokinase 3	_____________130___________142\n_____________\|_____________\|\n5'-UGA...UCGCU_____________CGUCU...UGC-3'\n______________CUGCGCC__CACC\n______________\|\|\|\|\|\|\|__\|\|\|\|\n______________GACGCGG__GUGG\n3'-UUU...CUUAU_______UU____UCCCU...GUG-5'\n_____________\|_____________\|\n_____________86____________72\n	131 -- 137	79 -- 85	-18.3373 kcal/mol	2.85158 kcal/mol	6.95176 kcal/mol	130 142@LB@ \| \|@LB@5'-UGA...UCGCU CGUCU...UGC-3'@LB@ CUGCGCC CACC@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ GACGCGG GUGG@LB@3'-UUU...CUUAU UU UCCCU...GUG-5'@LB@ \| \|@LB@ 86 72@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -18.3373 kcal/mol@LB@Unfolding Energy - mRNA 2.85158 kcal/mol@LB@Unfolding Energy - sRNA 6.95176 kcal/mol@LB@@LB@Position - mRNA 131 -- 141@LB@Position - sRNA 73 -- 85@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 79 -- 85@LB@
145	0.008374	0.2033	b0068	thiB	-7.61	0.367750	229 -- 244	73 -- 87	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein	_____________228______________245\n_____________\|________________\|\n5'-UUU...GCUGU________A_______CGUUU...ACU-3'\n______________UGCUGUGC_CAGCGCC\n______________\|:\|\|\|:\|\|_\|\|:\|:\|\|\n______________AUGACGCG_GUUGUGG\n3'-UUU...CGCUU________________UCCCU...GUG-5'\n_____________\|________________\|\n_____________88_______________72\n	230 -- 236	80 -- 86	-23.483 kcal/mol	8.91653 kcal/mol	6.95602 kcal/mol	228 245@LB@ \| \|@LB@5'-UUU...GCUGU A CGUUU...ACU-3'@LB@ UGCUGUGC CAGCGCC@LB@ \|:\|\|\|:\|\| \|\|:\|:\|\|@LB@ AUGACGCG GUUGUGG@LB@3'-UUU...CGCUU UCCCU...GUG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -7.61 kcal/mol@LB@Hybridization Energy -23.483 kcal/mol@LB@Unfolding Energy - mRNA 8.91653 kcal/mol@LB@Unfolding Energy - sRNA 6.95602 kcal/mol@LB@@LB@Position - mRNA 229 -- 244@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 80 -- 86@LB@
29	0.001588	0.1727	b4371	rsmC	-11.43	0.073969	145 -- 160	74 -- 89	16S rRNA m(2)G1207 methyltransferase SAM-dependent	_____________144______________161\n_____________\|________________\|\n5'-AUC...UCGUC_____C__________AUGGC...UGC-3'\n______________GAUAC_GCGCCAACAU\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|\|:\n______________UUAUG_CGCGGUUGUG\n3'-UUU...CGCGC_____A__________GUCCC...GUG-5'\n_____________\|________________\|\n_____________90_______________73\n	154 -- 160	74 -- 80	-22.1753 kcal/mol	3.46317 kcal/mol	7.27848 kcal/mol	144 161@LB@ \| \|@LB@5'-AUC...UCGUC C AUGGC...UGC-3'@LB@ GAUAC GCGCCAACAU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ UUAUG CGCGGUUGUG@LB@3'-UUU...CGCGC A GUCCC...GUG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -22.1753 kcal/mol@LB@Unfolding Energy - mRNA 3.46317 kcal/mol@LB@Unfolding Energy - sRNA 7.27848 kcal/mol@LB@@LB@Position - mRNA 145 -- 160@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 74 -- 80@LB@
39	0.002105	0.1727	b3249	mreD	-13.67	0.026871	102 -- 115	74 -- 87	cell wall structural complex MreBCD transmembrane component MreD	_____________101____________116\n_____________\|______________\|\n5'-CCU...GCGCC______________AGCCU...UUU-3'\n______________UGCUGCGCCGACAC\n______________\|:\|\|\|\|\|\|\|:\|\|\|\|\n______________AUGACGCGGUUGUG\n3'-UUU...CGCUU______________GUCCC...GUG-5'\n_____________\|______________\|\n_____________88_____________73\n	109 -- 115	74 -- 80	-25.8251 kcal/mol	5.39353 kcal/mol	6.75739 kcal/mol	101 116@LB@ \| \|@LB@5'-CCU...GCGCC AGCCU...UUU-3'@LB@ UGCUGCGCCGACAC@LB@ \|:\|\|\|\|\|\|\|:\|\|\|\|@LB@ AUGACGCGGUUGUG@LB@3'-UUU...CGCUU GUCCC...GUG-5'@LB@ \| \|@LB@ 88 73@LB@@LB@@LB@Energy -13.67 kcal/mol@LB@Hybridization Energy -25.8251 kcal/mol@LB@Unfolding Energy - mRNA 5.39353 kcal/mol@LB@Unfolding Energy - sRNA 6.75739 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 74 -- 87@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 74 -- 80@LB@
135	0.007679	0.1993	b0096	lpxC	-11.14	0.084212	289 -- 298	76 -- 85	UDP-3-O-acyl N-acetylglucosamine deacetylase	_____________288________299\n_____________\|__________\|\n5'-GAA...ACGCC__________CA-3'\n______________CUGCGCCGGC\n______________\|\|\|\|\|\|\|::\|\n______________GACGCGGUUG\n3'-UUU...CUUAU__________UGGUC...GUG-5'\n_____________\|__________\|\n_____________86_________75\n	292 -- 298	76 -- 82	-18.1767 kcal/mol	1.93848 kcal/mol	5.09564 kcal/mol	288 299@LB@ \| \|@LB@5'-GAA...ACGCC CA-3'@LB@ CUGCGCCGGC@LB@ \|\|\|\|\|\|\|::\|@LB@ GACGCGGUUG@LB@3'-UUU...CUUAU UGGUC...GUG-5'@LB@ \| \|@LB@ 86 75@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -18.1767 kcal/mol@LB@Unfolding Energy - mRNA 1.93848 kcal/mol@LB@Unfolding Energy - sRNA 5.09564 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 76 -- 85@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 76 -- 82@LB@
162	0.009519	0.2068	b4167	nnr	-8.70	0.240671	167 -- 176	76 -- 85	bifunctional NAD(P)H-hydrate repair enzyme; C-terminal domain ADP-dependent (S)-NAD(P)H-hydrate dehydratase and N-terminal domain NAD(P)H-hydrate epimerase	_____________166________177\n_____________\|__________\|\n5'-ACU...AUUUU__________UGAUU...UGC-3'\n______________UUGCGCUAAC\n______________:\|\|\|\|\|:\|\|\|\n______________GACGCGGUUG\n3'-UUU...CUUAU__________UGGUC...GUG-5'\n_____________\|__________\|\n_____________86_________75\n	170 -- 176	76 -- 82	-14.3794 kcal/mol	0.586298 kcal/mol	5.09564 kcal/mol	166 177@LB@ \| \|@LB@5'-ACU...AUUUU UGAUU...UGC-3'@LB@ UUGCGCUAAC@LB@ :\|\|\|\|\|:\|\|\|@LB@ GACGCGGUUG@LB@3'-UUU...CUUAU UGGUC...GUG-5'@LB@ \| \|@LB@ 86 75@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -14.3794 kcal/mol@LB@Unfolding Energy - mRNA 0.586298 kcal/mol@LB@Unfolding Energy - sRNA 5.09564 kcal/mol@LB@@LB@Position - mRNA 167 -- 176@LB@Position - sRNA 76 -- 85@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 76 -- 82@LB@
101	0.005473	0.1855	b1129	phoQ	-8.66	0.244665	211 -- 219	79 -- 87	sensory histidine kinase in two-component regulatory system with PhoP	_____________210_______220\n_____________\|_________\|\n5'-AUG...AAAAU_________UUUUU...GAA-3'\n______________UACUGCGUC\n______________\|\|\|\|\|\|\|:\|\n______________AUGACGCGG\n3'-UUU...CGCUU_________UUGUG...GUG-5'\n_____________\|_________\|\n_____________88________78\n	213 -- 219	79 -- 85	-14.7172 kcal/mol	1.01485 kcal/mol	5.0453 kcal/mol	210 220@LB@ \| \|@LB@5'-AUG...AAAAU UUUUU...GAA-3'@LB@ UACUGCGUC@LB@ \|\|\|\|\|\|\|:\|@LB@ AUGACGCGG@LB@3'-UUU...CGCUU UUGUG...GUG-5'@LB@ \| \|@LB@ 88 78@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -14.7172 kcal/mol@LB@Unfolding Energy - mRNA 1.01485 kcal/mol@LB@Unfolding Energy - sRNA 5.0453 kcal/mol@LB@@LB@Position - mRNA 211 -- 219@LB@Position - sRNA 79 -- 87@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 79 -- 85@LB@
167	0.009922	0.2071	b0367	tauC	-5.98	0.628340	152 -- 162	85 -- 95	taurine ABC transporter permease	_____________151_________163\n_____________\|___________\|\n5'-AUA...CGCCA___________GUUUU...UUU-3'\n______________UGCGCGAAUAU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________ACGCGCUUAUG\n3'-UUU...GCCCC___________ACGCG...GUG-5'\n_____________\|___________\|\n_____________96__________84\n	154 -- 160	87 -- 93	-16.0697 kcal/mol	4.17782 kcal/mol	5.90856 kcal/mol	151 163@LB@ \| \|@LB@5'-AUA...CGCCA GUUUU...UUU-3'@LB@ UGCGCGAAUAU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ ACGCGCUUAUG@LB@3'-UUU...GCCCC ACGCG...GUG-5'@LB@ \| \|@LB@ 96 84@LB@@LB@@LB@Energy -5.98 kcal/mol@LB@Hybridization Energy -16.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.17782 kcal/mol@LB@Unfolding Energy - sRNA 5.90856 kcal/mol@LB@@LB@Position - mRNA 152 -- 162@LB@Position - sRNA 85 -- 95@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 87 -- 93@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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