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
b4040	-14	-7	-13	-7	0.5	ChiX	44	51	44	50	0.84	-8.77	-10.11	-0.928883	AAGAGGAA&UUCCUCUU	((((((((&))))))))	CGAUUAAGCGGUAAACCGCUGUUGCUAACAGAACUGUUUUUACCGGCGUCACCGUUGUACUAAGAGGAAAAAAAUAUGGAGUGGAGUCUGACGCAGAAUAAGCUGCUGGCGUUUCAUCGCUUAAUGCGUACGGAUAAGCCAAUUGGCGCG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0322419	0.8602904	ubiA	948540	4-hydroxybenzoate octaprenyltransferase
b1740	59	72	59	65	2.83	ChiX	38	51	45	51	1.06	-8.84	-12.73	-0.936297	AAGAGGAAAUUCGU&AUGAAAUUCCUCUU	((((((((..((((&))))..))))))))	CCGCUGUCGCUUGUCGUUUCAGUAGCAACGGGUUAGCUUUAAGGAAGUUUUGUCUUUUCUGUCUGGAGGGGUUCAAUGACAUUGCAACAACAAAUAAUAAAGGCGCUGGGCGCAAAACCGCAGAUUAAUGCUGAAGAGGAAAUUCGUCGU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.031151	0.8602904	nadE	946946	NH3-dependent NAD(+) synthetase
b4255	-14	-6	-12	-6	0.69	ChiX	43	51	43	49	0.85	-10.02	-11.56	-1.06128	AAGAGGAAU&AUUCCUCUU	(((((((((&)))))))))	UUGUCACAAAGGUGGAGGCAAUGUCAGUGGUGUGUGACAAUAAGAGUAUCGGCAGGACAUUAAGAGGAAUGAGCCAUGGCAAACCCGGAACAACUGGAAGAACAGCGUGAAGAAACACGUUUGAUUAUUGAAGAAUUACUGGAAGAUGGC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0174928	0.8602904	rraB	948773	ribonuclease E inhibitor protein B
b1363	-74	-59	-74	-68	0.44	ChiX	36	51	45	51	1.07	-11.89	-13.4	-1.25934	AAGAGGAGUUAAAUUU&AAAUGAAAUUCCUCUU	((((((((((..((((&))))..))))))))))	UAAGAGGAGUUAAAUUUUAUACAGUAUAAUCAUAAUAUUGCAGCAAGGUGGUUAUAAUUGAAAGAAUAUUUAGAUAUGAAUACAUCUCAUGUAAGAGUUGUUACUCAUAUGUGUGGGUUCCUGGUUUGGCUCUAUAGUCUUUCAAUGUUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0071174	0.8602904	trkG	945932	Rac prophage K(+) transporter TrkG
b1561	38	73	60	66	6.89	ChiX	44	81	50	56	13.56	-8.75	-29.2	-0.926764	AAGAUGGCCUCUAUGCUGUGUGCGUUGAAAAUGGAA&UUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUU	(((((((((..((((((((...(((((((...((((&))))..))))))).....))))).)))..)))))))))	AAAUACUUAAGUAGCGCGCAGGGAUAAGAGGGAUGGUCCCUUAAAGGGGAGAGCUAAUUAUCCGGAAGGAUUCUGAUGAUGAACAUCGAAGAACUGCGUAAAAUUUUUUGUGAAGAUGGCCUCUAUGCUGUGUGCGUUGAAAAUGGAAAU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0325606	0.8602904	rem	946109	Qin prophage protein Rem
b3186	-14	-1	-10	-4	2.67	ChiX	38	51	41	47	1.06	-8.73	-12.46	-0.924646	AAGCGGAGUUUUAU&AUGAAAUUCCUCUU	(((.((((((((((&)))))))))).)))	UAUUCGCGCCCUAUUGUGAAUAUUUAUAGCGCACUCUGAAUCAUUGAAAAGGUGUGCGCGGAAGCGGAGUUUUAUAUGUACGCGGUUUUCCAAAGUGGUGGUAAACAACACCGAGUAAGCGAAGGUCAGACCGUUCGCCUGGAAAAGCUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0328826	0.8602904	rplU	949057	50S ribosomal subunit protein L21
b4047	-37	-30	-37	-31	0.3	ChiX	45	52	46	52	0.85	-8.42	-9.57	-0.891812	AAGGAGGA&UCCUCUUU	((((((((&))))))))	AGCGAUUUUUGAUAGUGACCAGAUGGCAAAAGAAUUAUAAGGAGGACACGGUACGACAAAAAAGGUAGAUGAAUCAUGUUGAAGAUAAUACCCGGUGCAACUGGAUACUUUAAUAAAACACUCAAUUCAAAUCAAUUCGAUAAUGAAGAU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.038306	0.8602904	yjbL	948551	uncharacterized protein YjbL
b3514	-12	2	-12	-6	3.02	ChiX	38	51	45	51	1.06	-9.59	-13.67	-1.01573	AAGGGGACUUUCAU&AUGAAAUUCCUCUU	(((((((.((((((&)))))).)))))))	CGAGCAAUUUCCUCCAGCCAGGAAAACGCCAGCACCGAAUCGAAACAAUAACGUUGCAGGCUUAAGGGGACUUUCAUGGCUAACUAUUUUAUUGAUCGCCCGGUUUUUGCCUGGGUACUUGCCAUUAUUAUGAUGCUUGCAGGUGGUCUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0215704	0.8602904	mdtF	948030	multidrug efflux pump RND permease MdtF
b0336	-13	-1	-10	-4	4.32	ChiX	40	52	43	49	0.93	-10.94	-16.19	-1.15872	AAGGGGGAAUUUC&GAAAUUCCUCUUU	(((((((((((((&)))))))))))))	CGAUUGCUUUUUAUCUUCAGAUGAAUAGAAUGCGGCGGAUUUUUUGGGUUUCAAACAGCAAAAAGGGGGAAUUUCGUGUCGCAAGAUAACAACUUUAGCCAGGGGCCAGUCCCGCAGUCGGCGCGGAAAGGGGUAUUGGCAUUGACGUUC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0112102	0.8602904	codB	944994	cytosine transporter
b0846	-14	-6	-14	-8	0.54	ChiX	44	52	46	52	0.86	-10.43	-11.83	-1.1047	AGAGAGGAA&UUCCUCUUU	(((((((((&)))))))))	UCAAAAUAAGAAGAGGGAAGACAACAUUAGCAAGGUUGUGUACAUUUGUACACAAUUGCAGAGAGAGGAAAUGACAUGCGUCGCGCUAACGAUCCGCAACGGCGAGAAAAAAUUAUCCAGGCCACGCUGGAGGCGGUGAAACUUUACGGA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0143379	0.8602904	rcdA	945473	DNA-binding transcriptional regulator RcdA

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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