Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
28	0.002284	0.2633	b1114	mfd	-18.81	0.004608	253 -- 297	50 -- 95	transcription-repair coupling factor	_____________252______________298\n_____________\|________________\|\n5'-UUC...GCGUC___U____________CGGCG...AAA-3'\n______________UGC_GGGCGAGUUAAC\n______________\|\|\|_:\|\|\|:\|\|\|:\|\|\|\n______________ACG_UCCGUUCAGUUG\n3'-UUU...GUACU________________AAAGU...UAG-5'\n_____________\|________________\|\n_____________96_______________49\n	262 -- 268	149 -- 155	-20.6961 kcal/mol	4.60584 kcal/mol	7.12854 kcal/mol	252 298@LB@ \| \|@LB@5'-UUC...GCGUC U CGGCG...AAA-3'@LB@ UGC GGGCGAGUUAAC@LB@ \|\|\| :\|\|\|:\|\|\|:\|\|\|@LB@ ACG UCCGUUCAGUUG@LB@3'-UUU...GUACU AAAGU...UAG-5'@LB@ \| \|@LB@ 96 49@LB@@LB@@LB@Energy -18.81 kcal/mol@LB@Hybridization Energy -20.6961 kcal/mol@LB@Unfolding Energy - mRNA 4.60584 kcal/mol@LB@Unfolding Energy - sRNA 7.12854 kcal/mol@LB@@LB@Position - mRNA 253 -- 297@LB@Position - sRNA 50 -- 95@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 149 -- 155@LB@
29	0.002294	0.2633	b0624	flc	-16.49	0.013425	233 -- 293	118 -- 176	fluoride efflux channel dual topology membrane protein	_____________232_____________________294\n_____________\|_______________________\|\n5'-AAA...CGGCG_______UA______C_______AAUCA...UUC-3'\n______________UUACACU_____UCA_UCAUACA\n______________\|\|\|\|\|\|:_____\|\|\|_\|\|\|:\|\|\|\n______________AAUGUGG_____AGU_AGUGUGU\n3'-UUU...ACUAA_______UUAUG___C_______ACUAC...UAG-5'\n_____________\|_______________________\|\n_____________177_____________________117\n	172 -- 178	167 -- 173	-16.8792 kcal/mol	2.93634 kcal/mol	5.08824 kcal/mol	232 294@LB@ \| \|@LB@5'-AAA...CGGCG UA C AAUCA...UUC-3'@LB@ UUACACU UCA UCAUACA@LB@ \|\|\|\|\|\|: \|\|\| \|\|\|:\|\|\|@LB@ AAUGUGG AGU AGUGUGU@LB@3'-UUU...ACUAA UUAUG C ACUAC...UAG-5'@LB@ \| \|@LB@ 177 117@LB@@LB@@LB@Energy -16.49 kcal/mol@LB@Hybridization Energy -16.8792 kcal/mol@LB@Unfolding Energy - mRNA 2.93634 kcal/mol@LB@Unfolding Energy - sRNA 5.08824 kcal/mol@LB@@LB@Position - mRNA 233 -- 293@LB@Position - sRNA 118 -- 176@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 167 -- 173@LB@
30	0.002398	0.2633	b0494	tesA	-12.69	0.080698	14 -- 26	126 -- 138	acyl-CoA thioesterase 1 and protease I and lysophospholipase L1	_____________13____________27\n_____________\|_____________\|\n5'-UCC...AUGUA_____________CAGAC...UGG-3'\n______________GCGGUUGUCCCAC\n______________\|\|\|\|\|::\|\|\|\|\|\|\n______________CGCCAGUAGGGUG\n3'-UUU...CUUAA_____________ACGUA...UAG-5'\n_____________\|_____________\|\n_____________139___________125\n	20 -- 26	126 -- 132	-24.3083 kcal/mol	5.59054 kcal/mol	8.249 kcal/mol	13 27@LB@ \| \|@LB@5'-UCC...AUGUA CAGAC...UGG-3'@LB@ GCGGUUGUCCCAC@LB@ \|\|\|\|\|::\|\|\|\|\|\|@LB@ CGCCAGUAGGGUG@LB@3'-UUU...CUUAA ACGUA...UAG-5'@LB@ \| \|@LB@ 139 125@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -24.3083 kcal/mol@LB@Unfolding Energy - mRNA 5.59054 kcal/mol@LB@Unfolding Energy - sRNA 8.249 kcal/mol@LB@@LB@Position - mRNA 14 -- 26@LB@Position - sRNA 126 -- 138@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 126 -- 132@LB@
31	0.002426	0.2633	b2593	yfiH	-12.28	0.097562	144 -- 222	126 -- 203	UPF0124 family protein	_____________143___________________________________________________________________________223\n_____________\|_____________________________________________________________________________\|\n5'-CCA...AUUGA______GC______________AAGA_____AG_____________G____GG___U____AA__U_A_________AGUGG...CAC-3'\n______________GGUGAU___GCGCCGAU_UUCG____ACAUA__GAUG_____AAGU_GACU__UUA_GAGU__GC_G_UUGUCCCGC\n______________\|\|\|\|\|\|___:\|:\|\|:\|\|_:\|\|:____\|\|\|:\|__\|\|\|\|_____\|\|\|\|_:\|\|\|__\|:\|_\|\|:\|__\|\|_\|_\|::\|\|\|\|:\|\n______________CCACUA___UGUGGUUA_GAGU____UGUGU__CUAC_____UUCA_UUGA__AGU_CUUA__CG_C_AGUAGGGUG\n3'-UUU...ACCGC______AAA________U____CAG______A_____GUCCG____G____A_________A___C___________ACGUA...UAG-5'\n_____________\|_____________________________________________________________________________\|\n_____________204___________________________________________________________________________125\n	216 -- 222	126 -- 132	-51.0225 kcal/mol	17.9985 kcal/mol	20.5417 kcal/mol	143 223@LB@ \| \|@LB@5'-CCA...AUUGA GC AAGA AG G GG U AA U A AGUGG...CAC-3'@LB@ GGUGAU GCGCCGAU UUCG ACAUA GAUG AAGU GACU UUA GAGU GC G UUGUCCCGC@LB@ \|\|\|\|\|\| :\|:\|\|:\|\| :\|\|: \|\|\|:\| \|\|\|\| \|\|\|\| :\|\|\| \|:\| \|\|:\| \|\| \| \|::\|\|\|\|:\|@LB@ CCACUA UGUGGUUA GAGU UGUGU CUAC UUCA UUGA AGU CUUA CG C AGUAGGGUG@LB@3'-UUU...ACCGC AAA U CAG A GUCCG G A A C ACGUA...UAG-5'@LB@ \| \|@LB@ 204 125@LB@@LB@@LB@Energy -12.28 kcal/mol@LB@Hybridization Energy -51.0225 kcal/mol@LB@Unfolding Energy - mRNA 17.9985 kcal/mol@LB@Unfolding Energy - sRNA 20.5417 kcal/mol@LB@@LB@Position - mRNA 144 -- 222@LB@Position - sRNA 126 -- 203@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 126 -- 132@LB@
32	0.002513	0.2642	b3456	livM	-11.89	0.117100	251 -- 271	186 -- 206	branched-chain amino acid ABC transporter permease	_____________250___________________________272\n_____________\|_____________________________\|\n5'-GCC...CUGCU______GCCG___________UG______CCGGA...CCA-3'\n______________GGUGAU_____ACCGGUAUUC__GGUCGC\n______________\|\|\|\|\|\|_____\|\|\|::\|\|:\|\|__:\|\|\|:\|\n______________CCACUA_____UGGUUAUGAG__UCAGUG\n3'-UUU...ACCGC______AAAUG__________________UGUAC...UAG-5'\n_____________\|_____________________________\|\n_____________207___________________________185\n	169 -- 175	176 -- 182	-27.5836 kcal/mol	14.0763 kcal/mol	5.03772 kcal/mol	250 272@LB@ \| \|@LB@5'-GCC...CUGCU GCCG UG CCGGA...CCA-3'@LB@ GGUGAU ACCGGUAUUC GGUCGC@LB@ \|\|\|\|\|\| \|\|\|::\|\|:\|\| :\|\|\|:\|@LB@ CCACUA UGGUUAUGAG UCAGUG@LB@3'-UUU...ACCGC AAAUG UGUAC...UAG-5'@LB@ \| \|@LB@ 207 185@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -27.5836 kcal/mol@LB@Unfolding Energy - mRNA 14.0763 kcal/mol@LB@Unfolding Energy - sRNA 5.03772 kcal/mol@LB@@LB@Position - mRNA 251 -- 271@LB@Position - sRNA 186 -- 206@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 176 -- 182@LB@
33	0.002591	0.2642	b0331	prpB	-22.44	0.000909	137 -- 159	1 -- 22	2-methylisocitrate lyase	_____________136__________________160\n_____________\|____________________\|\n5'-GUC...AUUGU_____A______________UUUAU...UGG-3'\n______________GGCAC_CCCCUUGCUUUGUC\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|\|\|::\|\|\n______________CCGUG_GGGGAACGAAGUAG\n3'-UUU...GUACC____________________-5'\n_____________\|___________________\|\n_____________23__________________1\n	153 -- 159	1 -- 7	-33.844 kcal/mol	4.2272 kcal/mol	8.43224 kcal/mol	136 160@LB@ \| \|@LB@5'-GUC...AUUGU A UUUAU...UGG-3'@LB@ GGCAC CCCCUUGCUUUGUC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|\|\|::\|\|@LB@ CCGUG GGGGAACGAAGUAG@LB@3'-UUU...GUACC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -22.44 kcal/mol@LB@Hybridization Energy -33.844 kcal/mol@LB@Unfolding Energy - mRNA 4.2272 kcal/mol@LB@Unfolding Energy - sRNA 8.43224 kcal/mol@LB@@LB@Position - mRNA 137 -- 159@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 1 -- 7@LB@
34	0.002769	0.2736	b2416	ptsI	-14.05	0.042463	178 -- 225	128 -- 177	PEP-protein phosphotransferase of PTS system (enzyme I)	_____________177_________________________________________226\n_____________\|___________________________________________\|\n5'-GUG...AAAAA_________AGUAAGGUAGGGU______UU______UU_____AUCCC...CCG-3'\n______________UCAGUCACA_____________UAUGAU__CAGGCA__UUAGC\n______________\|\|\|\|\|\|\|\|\|_____________:\|\|\|\|\|__\|\|\|\|\|\|__\|:\|:\|\n______________AGUCAGUGU_____________GUACUA__GUCCGU__AGUUG\n3'-UUU...UUAUG____________________________C_______UC_____AAAGU...UAG-5'\n_____________\|___________________________________________\|\n_____________178_________________________________________127\n	180 -- 186	169 -- 175	-30.6202 kcal/mol	5.78851 kcal/mol	8.17404 kcal/mol	177 226@LB@ \| \|@LB@5'-GUG...AAAAA AGUAAGGUAGGGU UU UU AUCCC...CCG-3'@LB@ UCAGUCACA UAUGAU CAGGCA UUAGC@LB@ \|\|\|\|\|\|\|\|\| :\|\|\|\|\| \|\|\|\|\|\| \|:\|:\|@LB@ AGUCAGUGU GUACUA GUCCGU AGUUG@LB@3'-UUU...UUAUG C UC AAAGU...UAG-5'@LB@ \| \|@LB@ 178 127@LB@@LB@@LB@Energy -14.05 kcal/mol@LB@Hybridization Energy -30.6202 kcal/mol@LB@Unfolding Energy - mRNA 5.78851 kcal/mol@LB@Unfolding Energy - sRNA 8.17404 kcal/mol@LB@@LB@Position - mRNA 178 -- 225@LB@Position - sRNA 128 -- 177@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 169 -- 175@LB@
35	0.002845	0.2736	b3887	dtd	-14.98	0.027287	55 -- 74	191 -- 211	D-tyr-tRNA(Tyr) deacylase	_____________54____________________75\n_____________\|_____________________\|\n5'-GGA...UCAUU______G______________CCCCA...UCG-3'\n______________UAUGGU_UGCUGGCGG_UGAU\n______________\|\|\|::\|_\|\|\|\|\|\|\|\|\|_\|\|\|\|\n______________AUAUUA_ACGACCGCC_ACUA\n3'-UUU...CGUCC______G_________C____AAAUG...UAG-5'\n_____________\|_____________________\|\n_____________212___________________190\n	64 -- 70	196 -- 202	-27.702 kcal/mol	6.2401 kcal/mol	11.5765 kcal/mol	54 75@LB@ \| \|@LB@5'-GGA...UCAUU G CCCCA...UCG-3'@LB@ UAUGGU UGCUGGCGG UGAU@LB@ \|\|\|::\| \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ AUAUUA ACGACCGCC ACUA@LB@3'-UUU...CGUCC G C AAAUG...UAG-5'@LB@ \| \|@LB@ 212 190@LB@@LB@@LB@Energy -14.98 kcal/mol@LB@Hybridization Energy -27.702 kcal/mol@LB@Unfolding Energy - mRNA 6.2401 kcal/mol@LB@Unfolding Energy - sRNA 11.5765 kcal/mol@LB@@LB@Position - mRNA 55 -- 74@LB@Position - sRNA 191 -- 211@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 196 -- 202@LB@
36	0.002935	0.2744	b3152	yraR	-13.11	0.066158	241 -- 255	123 -- 138	putative nucleoside-diphosphate-sugar epimerase	_____________240______________256\n_____________\|________________\|\n5'-ACU...GGUGG________________GGAUG...CGA-3'\n______________GCGGUCA_CCUGCUGC\n______________\|\|\|\|\|\|\|_\|\|::\|\|\|\|\n______________CGCCAGU_GGGUGACG\n3'-UUU...CUUAA_______A________UAGUC...UAG-5'\n_____________\|________________\|\n_____________139______________122\n	241 -- 247	132 -- 138	-26.7154 kcal/mol	6.55898 kcal/mol	13.7588 kcal/mol	240 256@LB@ \| \|@LB@5'-ACU...GGUGG GGAUG...CGA-3'@LB@ GCGGUCA CCUGCUGC@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\|@LB@ CGCCAGU GGGUGACG@LB@3'-UUU...CUUAA A UAGUC...UAG-5'@LB@ \| \|@LB@ 139 122@LB@@LB@@LB@Energy -13.11 kcal/mol@LB@Hybridization Energy -26.7154 kcal/mol@LB@Unfolding Energy - mRNA 6.55898 kcal/mol@LB@Unfolding Energy - sRNA 13.7588 kcal/mol@LB@@LB@Position - mRNA 241 -- 255@LB@Position - sRNA 123 -- 138@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 132 -- 138@LB@
37	0.00305	0.2773	b4084	alsK	-13.69	0.050122	28 -- 80	50 -- 101	D-allose kinase	_____________27__________________________________________________________81\n_____________\|___________________________________________________________\|\n5'-GCG...UACGA_____AG________G_________________________A__AAAAA___A_G____CAGGG...AAA-3'\n______________AAUUG__GU_GGACG_UU__CC__UGCAACCAG_GCAACUU_CG_____CUG_U_GCGG\n______________\|\|\|:\|__\|\|_\|\|\|\|\|_\|\|__\|\|__:\|\|\|\|\|\|\|\|_:\|\|\|\|\|\|_\|\|_____\|\|\|_\|_\|\|\|\|\n______________UUAGC__CA_CCUGC_AA__GG__GCGUUGGUC_UGUUGAA_GC_____GAC_A_CGCC\n3'-UUU...ACCAA_____AA__C_____G__UU__UU_________G____________________G____AUUUU...UAG-5'\n_____________\|___________________________________________________________\|\n_____________102_________________________________________________________49\n	56 -- 62	61 -- 67	-47.5504 kcal/mol	15.3524 kcal/mol	25.4279 kcal/mol	27 81@LB@ \| \|@LB@5'-GCG...UACGA AG G A AAAAA A G CAGGG...AAA-3'@LB@ AAUUG GU GGACG UU CC UGCAACCAG GCAACUU CG CUG U GCGG@LB@ \|\|\|:\| \|\| \|\|\|\|\| \|\| \|\| :\|\|\|\|\|\|\|\| :\|\|\|\|\|\| \|\| \|\|\| \| \|\|\|\|@LB@ UUAGC CA CCUGC AA GG GCGUUGGUC UGUUGAA GC GAC A CGCC@LB@3'-UUU...ACCAA AA C G UU UU G G AUUUU...UAG-5'@LB@ \| \|@LB@ 102 49@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -47.5504 kcal/mol@LB@Unfolding Energy - mRNA 15.3524 kcal/mol@LB@Unfolding Energy - sRNA 25.4279 kcal/mol@LB@@LB@Position - mRNA 28 -- 80@LB@Position - sRNA 50 -- 101@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 61 -- 67@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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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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