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
b3801	-75	-58	-67	-61	6.3	ChiX	40	55	43	49	1.01	-8.71	-16.02	-0.922528	GUCAGGGAGAGGGAUCUC&GAAAUUCCUCUUUGAC	((((...((((((((.((&)).)))))))).))))	GUCAGGGAGAGGGAUCUCAAUUAUCAAUGCUUAAUUACGUCAUCAUUUUGAUGACAUGAAACCGGAGCAUUUUGCAUGGAAUUUUCGUUUUCACCCAAACGUCUUGUUGUUGCUGUCGCCGCCGCUCUUCCUCUCAUGGCCAGCGCAGCA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0332077	0.8602904	aslA	949015	putative sulfatase AslA
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
b3141	41	51	41	47	3.69	ChiX	38	48	42	48	1.04	-8.7	-13.43	-0.921468	AGGAAUUUCAU&AUGAAAUUCCU	(((((((((((&)))))))))))	AAAGCGCAUCCGGUGCUGUUAAUCGGCGUGACUUUUGUGCUCUCUAUUGUUUGUUCCGCAUUCGGCAUUUUGUAAAUGGAACGAGGCACUGCGUCUGGUGGUGCCUCUUUACUUAAGGAAUUUCAUCCUGUGCAAACCCUUCAGCAAGUU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0333715	0.8602904	agaI	947985	putative deaminase AgaI
b2241	-12	-5	-11	-5	0.65	ChiX	43	50	43	49	0.84	-8.7	-10.19	-0.921468	AGAGGGAU&AUUCCUCU	((((((((&))))))))	GAAUAUGCGCGAAAUCAAACAAUUCAUGUUUUUACUAUGGCUAAAUGGUAAAAAACGAACUUCAGAGGGAUAACAAUGAAAACUCGCGACUCGCAAUCAAGUGACGUGAUUAUCAUUGGCGGCGGCGCAACGGGAGCCGGGAUUGCCCGC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0333715	0.8602904	glpA	946713	anaerobic glycerol-3-phosphate dehydrogenase subunit A
b1308	-75	-65	-74	-68	4.19	ChiX	40	50	43	49	0.92	-8.69	-13.8	-0.920409	AGGGGAGUUUC&GAAAUUCCUCU	(((((((((((&)))))))))))	AGGGGAGUUUCGCAAAAAUUGUUAAAUCUCAGGCGUAUAAUGGAUGGCAAUUUUCAUCCAUAGAAGGACGCUUACAUGUUUAAAAAAGGCUUACUUGCUCUGGCACUGGUGUUUUCACUGCCCGUUUUCGCCGCUGAACACUGGAUCGAU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0335361	0.8602904	pspE	945652	thiosulfate sulfurtransferase PspE
b0517	-18	-7	-18	-12	1.46	ChiX	45	56	50	56	0.93	-8.66	-11.05	-0.917232	CGUUAAAAAGGA&UCCUCUUUGACG	(((((((.((((&)))).)))))))	GAUCACAUAAUCCAGAUAUUUUCCCUGUAUGUUAAUUGCAGUCAUGCUUCACACCGUCGUUAAAAAGGAAGACAGAUGAAAAUCAGUCGGGAAACACUCCACCAGCUAAUUGAGAAUAAACUCUGCCAGGCUGGGUUAAAACGUGAGCAC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.034035	0.8602904	allD	948342	ureidoglycolate dehydrogenase
b0283	-13	-3	-10	-4	3.02	ChiX	44	54	45	51	0.93	-8.65	-12.6	-0.916173	UUAAGGAGGAA&UUCCUCUUUGA	(((((((((((&)))))))))))	AUUCGGGUACGGGAUUAUCCCAUCACUCUGGAUAAGCUGCUCGAUAAGCUGCCGGAUGUGGUUUAAGGAGGAACAAUGUCAUACCCGCUUUUUGACAAAGACGAACACUGGCAUAAGCCAGAGCAGGCGUUUCUCACCGAUGACCACCGG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0342029	0.8602904	paoD	945010	molybdenum cofactor insertion chaperone PaoD
b2014	-73	-61	-67	-61	2.9	ChiX	43	55	43	49	0.94	-8.57	-12.41	-0.907699	GUCGCUGAGGAAU&AUUCCUCUUUGAC	(((...(((((((&)))))))...)))	UUGUCGCUGAGGAAUCCAAAAAAAUGGGGCAAUUUUUUGCUUACGCGACGGUUAUCACCGUAAAGGAGAAUGACCAUGUCGCAUAACGUUACUCCAAACACCUCUCGCGUGGAAUUGCGUAAAACGCUUACGUUAGUUCCGGUUGUAAUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.035577	0.8602904	plaP	946533	putrescine:H(+) symporter PlaP
b3938	-20	-12	-18	-12	2.9	ChiX	45	53	45	51	0.91	-8.56	-12.37	-0.90664	CGAAGAGGA&UCCUCUUUG	(((((((((&)))))))))	GCGGGUUUACGGUCAGUACCCACAUCAACUGUGUGGUCUGGUCUCAAUUUAUUGACGAAGAGGAUUAAGUAUCUCAUGGCUGAAUGGAGCGGCGAAUAUAUCAGCCCAUACGCUGAGCACGGCAAGAAGAGUGAACAAGUCAAAAAGAUU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0357527	0.8602904	metJ	948435	DNA-binding transcriptional repressor MetJ
b4299	-15	-7	-13	-7	4.07	ChiX	45	53	45	51	0.91	-8.51	-13.49	-0.901344	CAAGGAGGA&UCCUCUUUG	(((((((((&)))))))))	CAGCAUGCUGAACAAAGCAUAUUUUCCACUAUGUAAUGCCGAUACCAUUUAUUCCAUGAGCAAGGAGGAGCCAUUAUGGUUCGCAAAGGGUGUAAUUCAUUAGUCCGUGCUGAAAAAAUAUUAACCCACAUUGCAUGGGUUGGUAUGGCA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0366442	0.8602904	yjhI	949100	KpLE2 phage-like element putative DNA-binding transcriptional regulator YjhI

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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