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
123	0.008923	0.2491	b3243	aaeR	-15.21	0.024673	72 -- 99	1 -- 34	transcriptional regulator for aaeXAB operon	_____________71_________________________________100\n_____________\|__________________________________\|\n5'-AAC...UGUCG________AA__________________C_____GAGAG...UCA-3'\n______________CCGCAGAG___GGGCAU____GGAAAGC_G_GGC\n______________\|\|:\|\|:\|:___\|\|:\|\|\|____\|:\|\|\|\|\|_\|_\|\|\|\n______________GGUGUUUU___CCUGUA____CUUUUCG_C_CCG\n3'-UUU...CCCGA________ACC______GUUU_______U_A___-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	88 -- 94	7 -- 13	-28.4227 kcal/mol	8.94529 kcal/mol	4.26884 kcal/mol	71 100@LB@ \| \|@LB@5'-AAC...UGUCG AA C GAGAG...UCA-3'@LB@ CCGCAGAG GGGCAU GGAAAGC G GGC@LB@ \|\|:\|\|:\|: \|\|:\|\|\| \|:\|\|\|\|\| \| \|\|\|@LB@ GGUGUUUU CCUGUA CUUUUCG C CCG@LB@3'-UUU...CCCGA ACC GUUU U A -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -28.4227 kcal/mol@LB@Unfolding Energy - mRNA 8.94529 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 72 -- 99@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 7 -- 13@LB@
81	0.004938	0.2139	b0115	aceF	-13.95	0.048783	266 -- 289	7 -- 31	pyruvate dehydrogenase dihydrolipoyltransacetylase component E2	_____________265_________________________290\n_____________\|___________________________\|\n5'-GAU...CUGGU_________C__________UU_____CGAAC...CGC-3'\n______________CAAAGUGGG_GACA___AAG__GAAGC\n______________\|\|\|\|:\|\|\|\|_\|\|\|\|___\|\|\|__:\|\|\|\|\n______________GUUUUACCC_CUGU___UUC__UUUCG\n3'-UUU...GAGGU______________AGU___U______UCACCG-5'\n_____________\|___________________________\|\n_____________32__________________________6\n	268 -- 274	23 -- 29	-21.1287 kcal/mol	4.65658 kcal/mol	2.52208 kcal/mol	265 290@LB@ \| \|@LB@5'-GAU...CUGGU C UU CGAAC...CGC-3'@LB@ CAAAGUGGG GACA AAG GAAGC@LB@ \|\|\|\|:\|\|\|\| \|\|\|\| \|\|\| :\|\|\|\|@LB@ GUUUUACCC CUGU UUC UUUCG@LB@3'-UUU...GAGGU AGU U UCACCG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -21.1287 kcal/mol@LB@Unfolding Energy - mRNA 4.65658 kcal/mol@LB@Unfolding Energy - sRNA 2.52208 kcal/mol@LB@@LB@Position - mRNA 266 -- 289@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 23 -- 29@LB@
179	0.01303	0.2504	b1276	acnA	-14.81	0.030801	184 -- 199	7 -- 22	aconitate hydratase 1; aconitase A	_____________183______________200\n_____________\|________________\|\n5'-CUU...ACCCU_U______________UAUGU...GCG-3'\n______________G_CAUUAAGGAGGAGC\n______________\|_\|\|\|:\|\|:\|\|::\|\|\|\n______________C_GUAGUUUCUUUUCG\n3'-UUU...UACCC_U______________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	193 -- 199	7 -- 13	-17.7225 kcal/mol	2.31939 kcal/mol	0.590875 kcal/mol	183 200@LB@ \| \|@LB@5'-CUU...ACCCU U UAUGU...GCG-3'@LB@ G CAUUAAGGAGGAGC@LB@ \| \|\|\|:\|\|:\|\|::\|\|\|@LB@ C GUAGUUUCUUUUCG@LB@3'-UUU...UACCC U UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -14.81 kcal/mol@LB@Hybridization Energy -17.7225 kcal/mol@LB@Unfolding Energy - mRNA 2.31939 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 184 -- 199@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 7 -- 13@LB@
200	0.01506	0.259	b0404	acpH	-14.03	0.046767	57 -- 80	6 -- 28	acyl carrier protein (ACP) phosphodiesterase; ACP hydrolyase	_____________56________________________81\n_____________\|_________________________\|\n5'-GCC...GGGAU______CA_________UUC_____AUUCA...GUU-3'\n______________AGUGGG___AUCAGGGA___GGGCA\n______________\|:\|\|\|\|___\|\|\|\|::\|\|___::\|\|\|\n______________UUACCC___UAGUUUCU___UUCGU\n3'-UUU...GUGUU______CUG________U_______CACCG-5'\n_____________\|_________________________\|\n_____________29________________________5\n	66 -- 72	12 -- 18	-19.5231 kcal/mol	4.78501 kcal/mol	0.706454 kcal/mol	56 81@LB@ \| \|@LB@5'-GCC...GGGAU CA UUC AUUCA...GUU-3'@LB@ AGUGGG AUCAGGGA GGGCA@LB@ \|:\|\|\|\| \|\|\|\|::\|\| ::\|\|\|@LB@ UUACCC UAGUUUCU UUCGU@LB@3'-UUU...GUGUU CUG U CACCG-5'@LB@ \| \|@LB@ 29 5@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -19.5231 kcal/mol@LB@Unfolding Energy - mRNA 4.78501 kcal/mol@LB@Unfolding Energy - sRNA 0.706454 kcal/mol@LB@@LB@Position - mRNA 57 -- 80@LB@Position - sRNA 6 -- 28@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 12 -- 18@LB@
16	0.0006527	0.1243	b2563	acpS	-16.60	0.010715	145 -- 164	1 -- 23	holo-[acyl-carrier-protein] synthase 1	_____________144_____________________165\n_____________\|_______________________\|\n5'-GCC...UGACC______G_____U__________AGAAA...GCG-3'\n______________GGAC_U_AAAGA___GCGGUGGC\n______________\|\|\|\|_\|_\|\|\|\|\|___\|\|:\|\|\|\|\|\n______________CCUG_A_UUUCU___CGUCACCG\n3'-UUU...UUACC____U_G_____UUU________-5'\n_____________\|______________________\|\n_____________24_____________________1\n	158 -- 164	1 -- 7	-25.7246 kcal/mol	7.54829 kcal/mol	1.57928 kcal/mol	144 165@LB@ \| \|@LB@5'-GCC...UGACC G U AGAAA...GCG-3'@LB@ GGAC U AAAGA GCGGUGGC@LB@ \|\|\|\| \| \|\|\|\|\| \|\|:\|\|\|\|\|@LB@ CCUG A UUUCU CGUCACCG@LB@3'-UUU...UUACC U G UUU -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -16.60 kcal/mol@LB@Hybridization Energy -25.7246 kcal/mol@LB@Unfolding Energy - mRNA 7.54829 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 145 -- 164@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 1 -- 7@LB@
77	0.004622	0.2062	b1241	adhE	-12.78	0.086641	182 -- 205	1 -- 21	fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase	_____________181______________________206\n_____________\|________________________\|\n5'-AAU...GUUUA______UC_________UUA____UGUUA...AAA-3'\n______________ACAUUA__AGGAGAGCA___UGGC\n______________\|\|\|\|:\|__\|\|:\|:\|\|\|\|___\|\|\|\|\n______________UGUAGU__UCUUUUCGU___ACCG\n3'-UUU...ACCCC______U__________C______-5'\n_____________\|_______________________\|\n_____________22______________________1\n	192 -- 198	6 -- 12	-20.8292 kcal/mol	6.5343 kcal/mol	1.51103 kcal/mol	181 206@LB@ \| \|@LB@5'-AAU...GUUUA UC UUA UGUUA...AAA-3'@LB@ ACAUUA AGGAGAGCA UGGC@LB@ \|\|\|\|:\| \|\|:\|:\|\|\|\| \|\|\|\|@LB@ UGUAGU UCUUUUCGU ACCG@LB@3'-UUU...ACCCC U C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -20.8292 kcal/mol@LB@Unfolding Energy - mRNA 6.5343 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 182 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 6 -- 12@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@
68	0.003723	0.191	b3131	agaR	-11.10	0.180958	280 -- 299	5 -- 22	transcriptional repressor of the aga regulon	_____________279__________________300\n_____________\|____________________\|\n5'-CAG...UCUGC____G________UGU____G-3'\n______________GACA_CAAGGGAG___GCAG\n______________\|\|\|\|_\|\|\|:\|:\|:___\|\|\|\|\n______________CUGU_GUUUCUUU___CGUC\n3'-UUU...UACCC____A________U______ACCG-5'\n_____________\|____________________\|\n_____________23___________________4\n	286 -- 292	10 -- 16	-17.5345 kcal/mol	4.90034 kcal/mol	1.53637 kcal/mol	279 300@LB@ \| \|@LB@5'-CAG...UCUGC G UGU G-3'@LB@ GACA CAAGGGAG GCAG@LB@ \|\|\|\| \|\|\|:\|:\|: \|\|\|\|@LB@ CUGU GUUUCUUU CGUC@LB@3'-UUU...UACCC A U ACCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -17.5345 kcal/mol@LB@Unfolding Energy - mRNA 4.90034 kcal/mol@LB@Unfolding Energy - sRNA 1.53637 kcal/mol@LB@@LB@Position - mRNA 280 -- 299@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 10 -- 16@LB@
8	0.0001267	0.05555	b2697	alaS	-16.66	0.010303	247 -- 274	1 -- 35	alanyl-tRNA synthetase	_____________246_________________________________275\n_____________\|___________________________________\|\n5'-CCA...CUUUU_______UAA______________________U__CAGCA...ACG-3'\n______________UCCAUAG____GGGACAUCA______GGUAGU_GC\n______________\|\|\|\|:\|:____\|\|\|\|\|\|\|\|\|______:\|:\|\|\|_\|\|\n______________AGGUGUU____CCCUGUAGU______UCGUCA_CG\n3'-UUU...ACCCG_______UUAC_________UUCUUU______C__-5'\n_____________\|__________________________________\|\n_____________36_________________________________1\n	259 -- 265	16 -- 22	-29.5579 kcal/mol	7.86268 kcal/mol	5.03645 kcal/mol	246 275@LB@ \| \|@LB@5'-CCA...CUUUU UAA U CAGCA...ACG-3'@LB@ UCCAUAG GGGACAUCA GGUAGU GC@LB@ \|\|\|\|:\|: \|\|\|\|\|\|\|\|\| :\|:\|\|\| \|\|@LB@ AGGUGUU CCCUGUAGU UCGUCA CG@LB@3'-UUU...ACCCG UUAC UUCUUU C -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -16.66 kcal/mol@LB@Hybridization Energy -29.5579 kcal/mol@LB@Unfolding Energy - mRNA 7.86268 kcal/mol@LB@Unfolding Energy - sRNA 5.03645 kcal/mol@LB@@LB@Position - mRNA 247 -- 274@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 16 -- 22@LB@
63	0.003337	0.1851	b1453	ansP	-14.01	0.047364	263 -- 293	1 -- 34	L-asparagine transporter	_____________262_________________________________294\n_____________\|___________________________________\|\n5'-GUC...AAUGC________A__________C_________AUG___AAUCGCC-3'\n______________CCACGAAG_GGGG_UAUCA____AAAGCG___GGC\n______________\|\|\|\|:\|\|:_\|\|\|\|_:\|\|\|\|____\|\|\|\|\|:___\|\|\|\n______________GGUGUUUU_CCCC_GUAGU____UUUCGU___CCG\n3'-UUU...CCCGA________A____U_____UUCU______CA____-5'\n_____________\|__________________________________\|\n_____________35_________________________________1\n	263 -- 269	28 -- 34	-31.7064 kcal/mol	13.4305 kcal/mol	4.26884 kcal/mol	262 294@LB@ \| \|@LB@5'-GUC...AAUGC A C AUG AAUCGCC-3'@LB@ CCACGAAG GGGG UAUCA AAAGCG GGC@LB@ \|\|\|\|:\|\|: \|\|\|\| :\|\|\|\| \|\|\|\|\|: \|\|\|@LB@ GGUGUUUU CCCC GUAGU UUUCGU CCG@LB@3'-UUU...CCCGA A U UUCU CA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -31.7064 kcal/mol@LB@Unfolding Energy - mRNA 13.4305 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 263 -- 293@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 28 -- 34@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)

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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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