Input and runtime details for job 8403881 (precomputed example)

Sequence Parameters

	Query ncRNA (short) in FASTA		[.fa]
	Index first query position		1
	Target RNA (long) in FASTA		[.fa]
	Target NCBI RefSeq ID		NC_000913
	All replicons		yes
	Extract sequences around		start codon
	nt upstream (1-300)		75
	nt downstream (1-300)		75
	Index first target position		-75

Output Parameters

	Number of interactions per RNA pair		1
	Suboptimal interaction overlap		can overlap in query
	Max. interaction length		not provided
	Max. absolute energy of an interaction		0
	Max. delta energy above mfe of an interaction		100
	No lonely base pairs		yes
	No GU at helix ends		yes

Seed Parameters

	Min. number of basepairs in seed		7
	Max. Number of mismatches in seed		0
	Maximal energy		0
	Minimal unpaired probability (per RNA)		0
	Seed position (query)		not provided
	Seed position (target)		not provided
	Ignore seeds with GU base pairs		no
	Ignore seeds with GU ends		yes

Folding Parameters

	Temperature for energy computation		37.0
	Access. query: folding window size		150
	Access. query: max. basepair distance		100
	Access. target: folding window size		150
	Access. target: max. basepair distance		100
	Energy parameter set (Vienna package)		Turner model, 2004

Job ID 8403881 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:15:25 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:18:18 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:19:13 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:20:45 CET 2020
	Job Completed		@ Mon Jan 27 14:20:57 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8403881&toolName=IntaRNA ( 30 days expiry )

Description of the job

RyhB - E. coli

Output [zip]

Downloadable files

	IntaRNA result table:		[csv]
	Target region plot		[png] [pdf]
	Query region plot		[png] [pdf]
	Functional enrichment file		[txt]
	Functional annotation chart		[html] [pdf] [png]

Target region plot

Query region plot

Function

Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Show rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all

Sort by selecting a column name.

Target	Start(T)	End(T)	Start(seed-T)	End(seed-T)	ED(T)	Query	Start(Q)	End(Q)	Start(seed-Q)	End(seed-Q)	ED(Q)	Energy	E(hybrid)	E_norm	RRI subseqs	RRI details	Seq(T)	Seq(Q)	p-value	fdr	gene	geneID	annotation
b2736	56	71	56	62	3.84	RyhB	38	59	53	59	3.27	-11.65	-18.76	-1.22497	UGGGAGCAGCACUGUC&GACAUUGCUCACAUUGCUUCCA	(((((((((((.((((&)))).))))......)))))))	CACCAUACCGUUAUCUUCCAGCGCUUAUAUUCACAAUAUCAAACAAAAUAUCACUUAAAUUAACAAGGAGAGCAGAUGAAAACGGGAUCUGAGUUUCAUGUCGGUAUCGUUGGCUUAGGGUCAAUGGGAAUGGGAGCAGCACUGUCAUAU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0198994	0.9496255	ygbJ	947200	putative dehydrogenase
b3365	-9	12	2	8	4.28	RyhB	38	57	42	48	3.21	-10.98	-18.47	-1.15452	GAGGCAAAAAUGAGCAAAGUC&GACAUUGCUCACAUUGCUUC	(((((((...(((((((..((&))..)))))))..)))))))	AAUUUGAUUUACAUCAAUAAGCGGGGUUGCUGAAUCGUUAAGGUAGGCGGUAAUAGAAAAGAAAUCGAGGCAAAAAUGAGCAAAGUCAGACUCGCAAUUAUCGGUAACGGUAUGGUCGGCCAUCGCUUUAUCGAAGAUCUUCUUGAUAAA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0282964	0.9496255	nirB	947868	nitrite reductase large subunit NAD(P)H-binding
b3867	-13	5	-6	1	8.94	RyhB	38	58	43	49	3.21	-10.87	-23.02	-1.14295	GGAAGGAGUGAGCAUGUC&GACAUUGCUCACAUUGCUUCC	(((((..(((((((((((&)))).)))))))....)))))	CAACCGGCUGAUGACCCGAAACGGGCAUCCGCCGGUACGCCGUAGCCGCCAGAGACGCCAUCGGAAGGAGUGAGCAUGUCUGUACAGCAAAUCGACUGGGAUCUGGCCCUGAUCCAGAAAUAUAACUAUUCCGGGCCACGAUACACCUCG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0299579	0.9496255	hemN	948362	coproporphyrinogen III oxidase SAM and NAD(P)H dependent oxygen-independent
b4255	-63	-43	-62	-56	5.2	RyhB	39	59	52	58	3.27	-18.09	-26.56	-1.90212	UGGAGGCAAUGUCAGUGGUGU&ACAUUGCUCACAUUGCUUCCA	((((((((((((.((((((((&)))))))).))))))))))))	UUGUCACAAAGGUGGAGGCAAUGUCAGUGGUGUGUGACAAUAAGAGUAUCGGCAGGACAUUAAGAGGAAUGAGCCAUGGCAAACCCGGAACAACUGGAAGAACAGCGUGAAGAAACACGUUUGAUUAUUGAAGAAUUACUGGAAGAUGGC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0004554	0.3956288	rraB	948773	protein inhibitor of RNase E
b0556	-10	11	1	7	5.95	RyhB	39	58	43	49	3.21	-12.89	-22.05	-1.35535	GGGGGCAACAGUGAGCAGAGU&ACAUUGCUCACAUUGCUUCC	((((((((..(((((((..((&))..))))))).))))))))	CGCUGGCGGUAAGCAAUGGAAAGGCCUGAUGACUCGUCGUGAGAUUGAGCGUGAAGUCUGUUUGUGGGGGCAACAGUGAGCAGAGUAACCGCGAUUAUAUCCGCUCUGAUUAUCUGCAUCAUCGUCAGCCUGUCAUGGGCGGUCAAUCAU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0101674	0.9496255	rzpD	945929	DLP12 prophage putative murein endopeptidase
b3219	-10	11	-9	-3	4.85	RyhB	39	59	52	58	3.27	-12.48	-20.6	-1.31224	UGGAGGCAAAAUGAACAAUGU&ACAUUGCUCACAUUGCUUCCA	(((((((((..((..((((((&))))))..))..)))))))))	AGCUUUUAAGGAUGAAGGGGAACUAACCGACAUGACAGAUAUUACAGGCAAUCUGACGGUCCUGGUGGAGGCAAAAUGAACAAUGUAAAAUUACUGAUUGCCGGAAGUGCCUUUUUUGCCAUGUCAGCGCAAGCCGCUGAUAGAGUAUCA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0127312	0.9496255	yhcF	947735	putative transcriptional regulator
b2727	-7	4	-6	1	4.77	RyhB	39	49	42	48	1.15	-12.05	-17.97	-1.26703	GUGAGCGAUGU&ACAUUGCUCAC	(((((((((((&)))))))))))	CAUGGUGACAUGCUGCAGAUUGUGGCAGACGACGGUUUACAGAUUCGGCGGAUAGAAAUAGACCAGGAGUGAGCGAUGUGUACAACAUGCGGUUGCGGUGAAGGCAACCUGUAUAUCGAGGGUGAUGAACAUAACCCUCAUUCCGCGUUU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0160688	0.9496255	hypB	947194	GTP hydrolase involved in nickel liganding into hydrogenases
b2550	-75	-66	-72	-66	1.49	RyhB	39	49	39	45	1.15	-11.07	-13.71	-1.16398	GUGGCAGUGU&ACAUUGCUCAC	((((((((((&))))))).)))	GUGGCAGUGUAUUGAACAAUCUGGCAAUGUUUUCGCGGAAUAAUCACGCAAUUAACUAAACAAGGUUUAGUGAAGAUGAGAGCCUGCAUUAAUAAUCAACAGAUUCGCCACCAUAACAAAUGCGUGAUUCUGGAACUGCUGUACCGGCAA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0270016	0.9496255	yphH	947023	putative DNA-binding transcriptional regulator
b4551	57	73	67	73	3.25	RyhB	39	58	39	45	3.21	-10.85	-17.31	-1.14085	GGAUUCAAUGGCGAUGU&ACAUUGCUCACAUUGCUUCC	(((..((((((((((((&)))))))...)))))..)))	GAGAUUUUCCAGCGUGAAAUGCAACAAGAACGACGCCAGCUGGACGGCUGGGAUGAAUUUGAGUAGAGGGUAAAGAUGGCAAUCCGAAAACGUUUUAUUGCGGGCGCAAAAUGCCCGGCCUGUCAGGCGCAGGAUUCAAUGGCGAUGUGG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0302697	0.9496255	yheV	1450290	DUF2387 family putative metal-binding protein
b4348	-73	-53	-59	-53	7.54	RyhB	40	66	40	46	3.3	-15.87	-26.71	-1.66869	GUGAACUGGGGGCGAGCGAUG&CAUUGCUCACAUUGCUUCCAGUAUUAC	(((((((((((((((((((((&)))))))).....))))))))).))))	GCGUGAACUGGGGGCGAGCGAUGAGGCCGAUUUGCAGCGUCAGUUGCUGGAAGAAGCGUUUGGUGGGGUGAAGGAAUGAGUGCGGGGAAAUUGCCGGAGGGGUGGGUUAUCGCCCCAGUAUCUACGGUCACAACUCUAAUCCGAGGAGUA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0018209	0.7909534	hsdS	948867	specificity determinant for hsdM and hsdR

Rows: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 all

Details of Selected Interaction Download Interaction Details

Target

Query

Energy

Hybridization Energy

Unfolding Energy - Target

Unfolding Energy - Query

Position - Target

Position - Query

Position Seed - Target

Position Seed - Query

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When using IntaRNA please cite :

Martin Mann, Patrick R. Wright, and Rolf Backofen
IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
Nucleic Acids Research, 2017, 45 (W1), W435–W439.
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.
Anke Busch, Andreas S. Richter, and Rolf Backofen
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Bioinformatics, 2008, 24 (24), 2849-56.
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 IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14

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