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
b1114	10	40	31	37	17.05	ChiX	46	73	49	55	11.33	-8.98	-37.36	-0.951125	CAAUAUCGUUAUACGCUGCCCGUCAAAGCGG&CCUCUUUGACGGGCCAAUAGCGAUAUUG	((((((((((((.....(((((((((((.((&)).)))))))))))..))))))))))))	UAAUGAACAGCAUUGCUUAUCAGAGAUAUGCCCCCAUAUGUUGAGGCAUAUCCUAACGAGAAUCUGACAACCGUUAUGCCUGAACAAUAUCGUUAUACGCUGCCCGUCAAAGCGGGUGAGCAGCGUCUGCUGGGCGAGUUAACCGGCGCA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0290804	0.8602904	mfd	945681	transcription-repair coupling factor
b1831	-42	2	-5	2	9.59	ChiX	38	75	38	44	13.6	-8.05	-31.24	-0.852623	GCCUGCGCUUGUUGGCUACGUCCGUUGUAAUCAGGAAAUUUCAU&AUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGC	(((..(((.(((((((..((((......((..((((.(((((((&)))))))))))..)))))).)))))))))).....)))	ACUGAUAGCGUCAUUAUAAUGACGCCUGUUCAUGCCUGCGCUUGUUGGCUACGUCCGUUGUAAUCAGGAAAUUUCAUGGAAAAUCAACCUAAGUUGAAUAGCAGUAAAGAAGUAAUCGCGUUUCUGGCCGAACGUUUUCCCCACUGUUUC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0459779	0.8602904	proQ	948950	RNA chaperone ProQ
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
b1476	-49	-27	-41	-35	5.65	ChiX	45	69	55	61	11.22	-11.4	-28.27	-1.20744	AUCGGUAUUGGCCCGAAUAAGGA&UCCUCUUUGACGGGCCAAUAGCGAU	((((.((((((((((((..((((&))))..))..)))))))))).))))	CUUUUGCCGGGUUGAUUUUCCACUACAUCGGUAUUGGCCCGAAUAAGGAAGUGGACGAUGACGAGGAGGAUCAUCAUGAGUAAGUCGAAAAUGAUUGUGCGCACCAAAUUUAUUGAUCGCGCCUGUCACUGGACCGUGGUGAUUUGCUUC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0089906	0.8602904	fdnI	946038	formate dehydrogenase N subunit gamma
b2483	-32	-8	-28	-22	6.92	ChiX	45	75	63	69	11.33	-8.27	-26.52	-0.875925	GCUAAUCGCUAUUGCCGUCUAAGGA&UCCUCUUUGACGGGCCAAUAGCGAUAUUGGC	(((((((((((((((((((..((((&))))....)))).)).)))))))))..))))	UUCGUCUCUAUUGCCUGUAUGUGGUCGCCGCACUGGUUGUGCUGCUAAUCGCUAUUGCCGUCUAAGGAAAUCACCAUGAGACAAACUCUUUGCGACGGAUAUCUGGUCAUUUUUGCGUUAGCACAGGCCGUGAUUCUGCUGAUGCUAACC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0412469	0.8602904	hyfC	947492	hydrogenase 4 component C
b1737	-67	-49	-66	-60	0.99	ChiX	38	56	49	55	1.17	-19.2	-21.36	-2.03359	CGUCAAAGAGUUAUUUCAU&AUGAAAUUCCUCUUUGACG	((((((((((..(((((((&)))))))..))))))))))	AAUUUUCCCGUCAAAGAGUUAUUUCAUAAAUCAAUACCGCAAUAUUUAAAUUGCGGUUUUUAAGGGUAUUUUUCUAUGAGUAAUGUUAUUGCAUCGCUUGAAAAGGUACUCCUCCCUUUUGCAGUUAAAAUAGGAAAGCAGCCACACGUU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0002604	0.7067256	chbC	945982	NN'-diacetylchitobiose-specific PTS enzyme IIC component
b0619	-37	-26	-35	-29	1.64	ChiX	46	57	49	55	2.73	-16.12	-20.49	-1.70736	CCGUCAAAGAGG&CCUCUUUGACGG	((((((((((((&))))))))))))	UAAUAUCUAUGUAUUUUGAUUCAACAUUUUAAUUACAUCCGUCAAAGAGGCUCGGGACAACCCGCAAGGAAAACAAUGUUGCAGCUUAACGAGAAUAAACAGUUUGCAUUUUUCCAAAGACUGGCAUUUCCGCUGCGUAUCUUUUUGCUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0010084	0.8602904	dpiB	945233	sensor histidine kinase DpiB
b4199	-17	-6	-15	-9	4.99	ChiX	46	57	49	55	2.73	-12.36	-20.08	-1.30912	CCGUCGAGGAGG&CCUCUUUGACGG	((((((((((((&))))))))))))	UUAUCAUUGAUUAAAAUUAAAUCAGAAGAUCAUCACAGAGGAGAGCACACAAAGUCAGCCGUCGAGGAGGUAUCUAUGUUCAGUCGUGUUUUAGCCCUUCUGGCUGUGCUUUUGCUAAGUGCAAAUACAUGGGCAGCCAUUGAAAUUAAU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0056965	0.8602904	yjfY	948713	DUF1471 domain-containing protein YjfY
b0681	-19	-8	-14	-8	2.71	ChiX	45	56	45	51	0.93	-15.8	-19.44	-1.67347	CGUCAAAGAGGA&UCCUCUUUGACG	((((((((((((&))))))))))))	CGCUACUUUUUUAAUUUUUAUUUUUUCGCUGUUCACCUUUGGUGCAGCAAUUUAUACGUCAAAGAGGAUUAACCCAUGCGUACGUUUAGUGGCAAACGUAGUACGCUGGCGCUGGCUAUCGCCGGUGUUACAGCAAUGUCGGGCUUUAUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0011645	0.8602904	chiP	945296	chitobiose outer membrane channel
b3118	-30	-14	-30	-24	6.52	ChiX	42	57	51	57	2.73	-8.84	-18.09	-0.936297	CCGUCAAUGAGGUAAUU&AAUUCCUCUUUGACGG	(((((((.((((.((((&)))))))).)))))))	AGUGGUCGCACAUAUCCUGUUCAUUUCAUUUUGAUACACUUCAUGCCGUCAAUGAGGUAAUUAACGUAGGUCGUUAUGAGCACUAUUCUUCUUCCGAAAACGCAGCACCUGGUAGUCUUUCAGGAAGUCAUUAGAAGUGGUUCUAUCGGC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.031151	0.8602904	tdcA	947494	DNA-binding transcriptional activator TdcA

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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