Input and runtime details for job 6244847 (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 6244847 (server version trunk)

	Job Submitted & Queued		@ Fri Jan 07 21:36:19 CET 2022
	Pre-Processing Started		@ Fri Jan 07 21:36:23 CET 2022
	IntaRNA Started		@ Fri Jan 07 21:38:06 CET 2022
	IntaRNA Finished & Post-Processing		@ Fri Jan 07 21:38:48 CET 2022
	Post-Processing Finished		@ Fri Jan 07 21:39:11 CET 2022
	Job Completed		@ Fri Jan 07 21:39:12 CET 2022

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6244847&toolName=IntaRNA ( 30 days expiry )

Description of the job

ChiX - 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
b2962	-14	-7	-13	-7	0.54	ChiX	45	52	45	51	0.85	-8.71	-10.1	-0.922528	AAAGAGGA&UCCUCUUU	((((((((&))))))))	CCCGUGGAGCGUUUGUUACAGCAGUUACGCACUGGCGCGCCGGUUUAGCGCGUGAGUCGAUAAAGAGGAUGAUUUAUGAGCAGAACGAUUUUUUGUACUUUCCUGCAACGUGAAGCAGAAGGUCAGGAUUUUCAGCUGUACCCCGGCGAG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0332077	0.8602904	yggX	947461	putative Fe(2(+))-trafficking protein
b0440	-16	-8	-15	-9	0.56	ChiX	44	52	45	51	0.86	-9.36	-10.78	-0.991373	AAAGAGGAA&UUCCUCUUU	(((((((((&)))))))))	GGCCUGAUAUAACUGCUGCGCGUUCGUACCUUGAAGGAUUCAAGUGCGAUAUAAAUUAUAAAGAGGAAGAGAAGAGUGAAUAAAUCUCAAUUGAUCGACAAGAUUGCUGCAGGGGCUGAUAUCUCUAAAGCUGCGGCUGGCCGUGCGUUA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0241376	0.8602904	hupB	949095	DNA-binding protein HU-beta
b1474	-13	-5	-12	-6	1.53	ChiX	44	52	45	51	0.86	-9.28	-11.67	-0.9829	AAAGAGGAA&UUCCUCUUU	(((((((((&)))))))))	AUUUCGCGCAAAAAGAUUCAGAAUUUUACUGUUAGUUUCCUCGCGCAGUAAUACCCCUGAAAAAAGAGGAAAGCAAUGGACGUCAGUCGCAGACAAUUUUUUAAAAUCUGCGCGGGCGGUAUGGCUGGAACAACAGUAGCGGCAUUGGGC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0251018	0.8602904	fdnG	946035	formate dehydrogenase N subunit alpha
b1550	-12	-4	-12	-6	1.88	ChiX	44	52	46	52	0.86	-8.87	-11.61	-0.939474	AAAGAGGAA&UUCCUCUUU	(((((((((&)))))))))	AUCUUUUACACGUUUGCACCAUAUAAUCGACUUACUGUGUAACUGGAAAGUCAUAACAGACUAAAAGAGGAAAUGAUGAAUAUUGAAAACUUAAAAACAAAAGCAGAAGCAGAUAUUUCUGAAUAUAUAACAAAAAAAAUUAUUGAACUU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0306951	0.8602904	gnsB	946054	Qin prophage protein GnsB
b2457	-15	-7	-14	-8	1.38	ChiX	44	52	45	51	0.86	-8.82	-11.06	-0.934178	AAAGAGGAA&UUCCUCUUU	(((((((((&)))))))))	GAACCGCGAAAGCAGUUUACAAACACUGGUUGAAUGAACGGUCCCGUUCUGGACCCUGAUAAAGAGGAAAGCACAAUGGAAGCAUUAGGAAUGAUCGAAACCCGGGGCCUGGUUGCACUGAUUGAGGCUUCUGACGCGAUGGUGAAAGCU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0314588	0.8602904	eutM	946942	putative ethanolamine catabolic microcompartment shell protein EutM
b1093	-13	2	-12	-6	1.42	ChiX	38	52	45	51	1.06	-11.48	-13.96	-1.21591	AAAGAGGAAAAUCAU&AUGAAAUUCCUCUUU	(((((((((..((((&))))..)))))))))	GACACCCUGACCGCCUCGGCGCUGAACGAACCUUCAGCGAUGGCAGCGGCGCUCGAGCUUUAAAAGAGGAAAAUCAUGAAUUUUGAAGGAAAAAUCGCACUGGUAACCGGUGCAAGCCGCGGAAUUGGCCGCGCAAUUGCUGAAACGCUC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0086532	0.8602904	fabG	945645	3-oxoacyl-[acyl-carrier-protein] reductase FabG
b0526	34	45	35	41	4.07	ChiX	41	52	45	51	0.86	-9.83	-14.76	-1.04115	AAAGAGGAAUUU&AAAUUCCUCUUU	((((((((((((&))))))))))))	GUAUGCUGAUUCGCGCGGGAAAUAUGGGUAUUAUACGCAACUCAAUUACCCACACAUGUCUAAACGGAAUCUUCGAUGCUAAAAAUCUUCAAUACUCUGACACGCCAAAAAGAGGAAUUUAAGCCUAUUCACGCCGGGGAAGUCGGCAUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0191875	0.8602904	cysS	946969	cysteine--tRNA ligase
b1257	-15	2	-14	-8	4.93	ChiX	38	52	45	51	1.06	-8.11	-14.1	-0.858978	AAAGAGGACAUUUUCAU&AUGAAAUUCCUCUUU	((((((((...((((((&)))))).))))))))	GUAAAUAAGAAAGCCGAAAAUAAAGCCUGAAAUAUGAAUUUUAACUUUUAGUCAUUUUAUAAAGAGGACAUUUUCAUGAAUCGUAUUGAACAUUAUCAUGACUGGUUACGUGACGCCCACGCAAUGGAAAAGCAAGCCGAAUCUAUGCUU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0446359	0.8602904	yciE	946871	DUF892 domain-containing protein YciE
b1040	-16	-2	-11	-5	4.15	ChiX	38	52	41	47	1.06	-9.19	-14.4	-0.973367	AAAGCGGGGUUUCAU&AUGAAAUUCCUCUUU	((((.((((((((((&)))))))))).))))	UGUCAGUACUUCUGGUGCUUCUAUUUUAGAGGCAGCUGUCAGGUGUGCGAUCAAUAAAAAAAGCGGGGUUUCAUCAUGUUUAAUGAAGUCCAUAGUAUUCAUGGUCAUACAUUAUUGUUGAUCACUAAAUCUUCUUUGCAGGCGACAGCU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0262335	0.8602904	csgD	949119	DNA-binding transcriptional dual regulator CsgD
b2204	-49	-39	-48	-42	1.47	ChiX	42	52	45	51	0.86	-9.73	-12.06	-1.03056	AAAGGGGAGUU&AAUUCCUCUUU	(((((((((((&)))))))))))	UCAAGGUGUUACCGCUGUCACUGGCGAAAGGGGAGUUAGGUCACCAUUACCGCUUCGGCUGGCUGGAGGGGAACAAUGGCAAAUCGUAAACGUGACGCCGGGCGCGAGGCGCUGGAGAAAAAAGGCUGGUGGCGCAGUCACCGUUGGCUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0201459	0.8602904	napH	945984	ferredoxin-type protein NapH

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 3.2.0 linking Vienna RNA package 2.4.14

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