Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
45	0.009513	0.5385	b2513	yfgM	-9.58	0.124672	177 -- 189	15 -- 27	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________176___________190\n_____________\|_____________\|\n5'-GGC...UUACU_________A___AGAAG...UUG-3'\n______________GGGUUAAGG_AGG\n______________\|\|\|\|\|\|\|::_\|\|\|\n______________CCCAAUUUU_UCC\n3'-CGC...AAGUU_________C___ACGGC...AAG-5'\n_____________\|_____________\|\n_____________28____________14\n	179 -- 185	19 -- 25	-14.0675 kcal/mol	1.24912 kcal/mol	3.23583 kcal/mol	176 190@LB@ \| \|@LB@5'-GGC...UUACU A AGAAG...UUG-3'@LB@ GGGUUAAGG AGG@LB@ \|\|\|\|\|\|\|:: \|\|\|@LB@ CCCAAUUUU UCC@LB@3'-CGC...AAGUU C ACGGC...AAG-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -9.58 kcal/mol@LB@Hybridization Energy -14.0675 kcal/mol@LB@Unfolding Energy - mRNA 1.24912 kcal/mol@LB@Unfolding Energy - sRNA 3.23583 kcal/mol@LB@@LB@Position - mRNA 177 -- 189@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 19 -- 25@LB@
178	0.03115	0.5559	b2528	iscA	-9.66	0.120899	187 -- 207	62 -- 80	FeS cluster assembly protein	_____________186___________________208\n_____________\|_____________________\|\n5'-UUC...UAAGA____A_G_________G____UUACA...CCG-3'\n______________GUUG_G_UUUGGUUAU_UCGA\n______________\|\|\|\|_\|_\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CAAC_C_AAAUCAAUA_AGCU\n3'-CGC...AAGUG______G______________CAACU...AAG-5'\n_____________\|_____________________\|\n_____________81____________________61\n	196 -- 202	66 -- 72	-17.7068 kcal/mol	7.30815 kcal/mol	0.737855 kcal/mol	186 208@LB@ \| \|@LB@5'-UUC...UAAGA A G G UUACA...CCG-3'@LB@ GUUG G UUUGGUUAU UCGA@LB@ \|\|\|\| \| \|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CAAC C AAAUCAAUA AGCU@LB@3'-CGC...AAGUG G CAACU...AAG-5'@LB@ \| \|@LB@ 81 61@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -17.7068 kcal/mol@LB@Unfolding Energy - mRNA 7.30815 kcal/mol@LB@Unfolding Energy - sRNA 0.737855 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 62 -- 80@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 66 -- 72@LB@
43	0.009109	0.5385	b2531	iscR	-9.39	0.134324	275 -- 298	62 -- 87	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________274________________________299\n_____________\|__________________________\|\n5'-AUG...GGCCC___A__________GAUAUUUC____AC-3'\n______________GGU_C_CGUUGGCU_________CGA\n______________:\|\|_\|_\|\|\|\|\|\|\|\|_________\|\|\|\n______________UCA_G_GCAACCGA_________GCU\n3'-CGC...CGUUU___A_U________AAUCAAUAA___CAACU...AAG-5'\n_____________\|__________________________\|\n_____________88_________________________61\n	281 -- 287	74 -- 80	-16.3089 kcal/mol	5.20915 kcal/mol	1.70771 kcal/mol	274 299@LB@ \| \|@LB@5'-AUG...GGCCC A GAUAUUUC AC-3'@LB@ GGU C CGUUGGCU CGA@LB@ :\|\| \| \|\|\|\|\|\|\|\| \|\|\|@LB@ UCA G GCAACCGA GCU@LB@3'-CGC...CGUUU A U AAUCAAUAA CAACU...AAG-5'@LB@ \| \|@LB@ 88 61@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -16.3089 kcal/mol@LB@Unfolding Energy - mRNA 5.20915 kcal/mol@LB@Unfolding Energy - sRNA 1.70771 kcal/mol@LB@@LB@Position - mRNA 275 -- 298@LB@Position - sRNA 62 -- 87@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 74 -- 80@LB@
176	0.03112	0.5559	b2536	hcaT	-7.63	0.261550	240 -- 259	67 -- 85	putative 3-phenylpropionic transporter	_____________239__________________260\n_____________\|____________________\|\n5'-UCG...GCUAU_____AUACUU_________CGGCA...GGA-3'\n______________UUCAC______UUUUAGUUA\n______________\|\|\|\|\|______:\|\|\|\|\|\|\|\|\n______________AAGUG______GAAAUCAAU\n3'-CGC...UUUUC_____CAACC__________AAGCU...AAG-5'\n_____________\|____________________\|\n_____________86___________________66\n	253 -- 259	67 -- 73	-10.0019 kcal/mol	1.80629 kcal/mol	0.569003 kcal/mol	239 260@LB@ \| \|@LB@5'-UCG...GCUAU AUACUU CGGCA...GGA-3'@LB@ UUCAC UUUUAGUUA@LB@ \|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ AAGUG GAAAUCAAU@LB@3'-CGC...UUUUC CAACC AAGCU...AAG-5'@LB@ \| \|@LB@ 86 66@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -10.0019 kcal/mol@LB@Unfolding Energy - mRNA 1.80629 kcal/mol@LB@Unfolding Energy - sRNA 0.569003 kcal/mol@LB@@LB@Position - mRNA 240 -- 259@LB@Position - sRNA 67 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 67 -- 73@LB@
123	0.02095	0.5385	b2562	yfhL	-10.74	0.078719	174 -- 195	59 -- 77	putative 4Fe-4S cluster-containing protein	_____________173____________________196\n_____________\|______________________\|\n5'-AGC...CGCCC_____GU_______UGA_____UCCUU...UUA-3'\n______________GGUUU__GUUGUUU___GAGUU\n______________\|\|:\|\|__\|\|\|:\|\|:___\|\|\|\|\|\n______________CCGAA__CAAUAAG___CUCAA\n3'-CGC...UGCAA_____AU_______________CUCUU...AAG-5'\n_____________\|______________________\|\n_____________78_____________________58\n	181 -- 187	64 -- 70	-15.8972 kcal/mol	4.34594 kcal/mol	0.811926 kcal/mol	173 196@LB@ \| \|@LB@5'-AGC...CGCCC GU UGA UCCUU...UUA-3'@LB@ GGUUU GUUGUUU GAGUU@LB@ \|\|:\|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ CCGAA CAAUAAG CUCAA@LB@3'-CGC...UGCAA AU CUCUU...AAG-5'@LB@ \| \|@LB@ 78 58@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -15.8972 kcal/mol@LB@Unfolding Energy - mRNA 4.34594 kcal/mol@LB@Unfolding Energy - sRNA 0.811926 kcal/mol@LB@@LB@Position - mRNA 174 -- 195@LB@Position - sRNA 59 -- 77@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 64 -- 70@LB@
145	0.02443	0.5467	b2569	lepA	-12.53	0.038132	5 -- 17	71 -- 85	back-translocating elongation factor EF4 GTPase	_____________4_______________18\n_____________\|_______________\|\n_______5'-UGAU_______________UUGCA...ACC-3'\n______________UUCAC__UGGCUUUG\n______________\|\|\|\|\|__\|\|\|\|\|\|\|:\n______________AAGUG__ACCGAAAU\n3'-CGC...UUUUC_____CA________CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	11 -- 17	71 -- 77	-14.3569 kcal/mol	1.27074 kcal/mol	0.560731 kcal/mol	4 18@LB@ \| \|@LB@ 5'-UGAU UUGCA...ACC-3'@LB@ UUCAC UGGCUUUG@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ AAGUG ACCGAAAU@LB@3'-CGC...UUUUC CA CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -14.3569 kcal/mol@LB@Unfolding Energy - mRNA 1.27074 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 5 -- 17@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 71 -- 77@LB@
113	0.0192	0.5385	b2573	rpoE	-9.32	0.137991	165 -- 193	49 -- 83	RNA polymerase sigma E factor	_____________164___________________________________194\n_____________\|_____________________________________\|\n5'-ACA...GAUAG________AAA_______UG_________________ACCUC...UGG-3'\n______________CGCG_UGG___UUUGGUU_________GGGAGACUUU\n______________\|:\|\|_\|\|\|___\|\|\|:\|\|\|_________\|:\|\|:\|\|\|:\|\n______________GUGC_ACC___AAAUCAA_________CUCUUUGAGA\n3'-CGC...UUCAA____A___G_________UAAGCUCAA__________GCUUU...AAG-5'\n_____________\|_____________________________________\|\n_____________84____________________________________48\n	184 -- 190	52 -- 58	-21.709 kcal/mol	7.98 kcal/mol	4.40602 kcal/mol	164 194@LB@ \| \|@LB@5'-ACA...GAUAG AAA UG ACCUC...UGG-3'@LB@ CGCG UGG UUUGGUU GGGAGACUUU@LB@ \|:\|\| \|\|\| \|\|\|:\|\|\| \|:\|\|:\|\|\|:\|@LB@ GUGC ACC AAAUCAA CUCUUUGAGA@LB@3'-CGC...UUCAA A G UAAGCUCAA GCUUU...AAG-5'@LB@ \| \|@LB@ 84 48@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -21.709 kcal/mol@LB@Unfolding Energy - mRNA 7.98 kcal/mol@LB@Unfolding Energy - sRNA 4.40602 kcal/mol@LB@@LB@Position - mRNA 165 -- 193@LB@Position - sRNA 49 -- 83@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 52 -- 58@LB@
58	0.01138	0.5385	b2595	bamD	-7.85	0.240744	21 -- 29	72 -- 80	BamABCDE complex OM biogenesis lipoprotein	_____________20________30\n_____________\|_________\|\n5'-CUG...ACCGA_________CGGAC...AUG-3'\n______________GUUGGUUUU\n______________\|\|\|\|\|:\|\|\|\n______________CAACCGAAA\n3'-CGC...AAGUG_________UCAAU...AAG-5'\n_____________\|_________\|\n_____________81________71\n	23 -- 29	72 -- 78	-10.2023 kcal/mol	2.1418 kcal/mol	0.205868 kcal/mol	20 30@LB@ \| \|@LB@5'-CUG...ACCGA CGGAC...AUG-3'@LB@ GUUGGUUUU@LB@ \|\|\|\|\|:\|\|\|@LB@ CAACCGAAA@LB@3'-CGC...AAGUG UCAAU...AAG-5'@LB@ \| \|@LB@ 81 71@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -10.2023 kcal/mol@LB@Unfolding Energy - mRNA 2.1418 kcal/mol@LB@Unfolding Energy - sRNA 0.205868 kcal/mol@LB@@LB@Position - mRNA 21 -- 29@LB@Position - sRNA 72 -- 80@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 72 -- 78@LB@
111	0.01894	0.5385	b2600	tyrA	-7.88	0.238290	191 -- 206	74 -- 89	fused chorismate mutase T/prephenate dehydrogenase	_____________190______________207\n_____________\|________________\|\n5'-UCG...CUUAA_________UA_____GCUGA...UGG-3'\n______________GAGGUUUAU__UGGUU\n______________:\|:\|\|\|:\|:__\|\|\|:\|\n______________UUUCAAGUG__ACCGA\n3'-CGC...GGCGU_________CA_____AAUCA...AAG-5'\n_____________\|________________\|\n_____________90_______________73\n	193 -- 199	81 -- 87	-12.4695 kcal/mol	4.06959 kcal/mol	0.517373 kcal/mol	190 207@LB@ \| \|@LB@5'-UCG...CUUAA UA GCUGA...UGG-3'@LB@ GAGGUUUAU UGGUU@LB@ :\|:\|\|\|:\|: \|\|\|:\|@LB@ UUUCAAGUG ACCGA@LB@3'-CGC...GGCGU CA AAUCA...AAG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.4695 kcal/mol@LB@Unfolding Energy - mRNA 4.06959 kcal/mol@LB@Unfolding Energy - sRNA 0.517373 kcal/mol@LB@@LB@Position - mRNA 191 -- 206@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 81 -- 87@LB@
109	0.0187	0.5385	b2616	recN	-10.46	0.088138	200 -- 208	75 -- 83	recombination and repair protein	_____________199_______209\n_____________\|_________\|\n5'-UGA...ACGAC_________ACAAC...CGG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	202 -- 208	75 -- 81	-13.4657 kcal/mol	2.51607 kcal/mol	0.492259 kcal/mol	199 209@LB@ \| \|@LB@5'-UGA...ACGAC ACAAC...CGG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -13.4657 kcal/mol@LB@Unfolding Energy - mRNA 2.51607 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 200 -- 208@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 75 -- 81@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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