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
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
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
b2768	44	53	46	52	1.52	ChiX	48	57	49	55	2.73	-8.45	-12.7	-0.894989	CCGUUAAAGA&UCUUUGACGG	((((((((((&))))))))))	CACUACAACAGUGGCGCUAUCCGCCUUCCGGAUUCGGCAUCACCUACCGCUUUGGAUAAAUAAUAAGGAUAAUUUAUGCCCCUCUUACACCUGCUCCGCCAGAAUCCGGUGAUUGCUGCCGUUAAAGAUAAUGCCAGCCUGCAACUGGCA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0377438	0.8602904	ygcP	947536	putative anti-terminator regulatory protein
b3133	-16	-7	-14	-8	0.77	ChiX	44	53	45	51	0.92	-12.48	-14.17	-1.32183	CAAAGAGGAA&UUCCUCUUUG	((((((((((&))))))))))	ACCAUAUUCAGGACAUCCUGGCGCAGUACCACACAGCCUGUGAAGGCCAAUAAGCAAAACAAAGAGGAACACGCUAUGCCAAAUAUUGUUUUAAGCCGGAUUGAUGAACGCUUGAUUCACGGUCAGGUCGGCGUUCAAUGGGUCGGAUUU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0053828	0.8602904	agaV	947648	N-acetyl-D-galactosamine specific PTS enzyme IIB component
b3176	-68	-60	-67	-61	1.53	ChiX	48	56	49	55	0.89	-9.42	-11.84	-0.997728	CGUCAAAGA&UCUUUGACG	(((((((((&)))))))))	UUCAUGACGUCAAAGAAACCGUAGAAGCGAUGCGGGUGGUGGAAGCCACUCUGUCUGCAAAGGAAAACAAACGCUAUGAGUAAUCGUAAAUAUUUCGGUACCGAUGGGAUUCGUGGUCGUGUAGGGGAUGCGCCGAUCACACCUGAUUUU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0234392	0.8602904	glmM	947692	phosphoglucosamine mutase
b3287	-68	-55	-63	-57	6.09	ChiX	41	54	43	49	0.94	-10.56	-17.59	-1.11847	UCAGAGGGGGAUUU&AAAUUCCUCUUUGA	((((((((((((((&))))))))))))))	CUGUCAAUCAGAGGGGGAUUUGUCUAGAAUAGAAGAAAUAAUCUUUCUAACUCCUGAACACAUCUCUGGAGAUUUAUGUCAGUUUUGCAAGUGUUACAUAUUCCGGACGAGCGGCUUCGCAAAGUUGCUAAACCGGUAGAAGAAGUGAAU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0134642	0.8602904	def	947780	peptide deformylase
b3304	-31	-24	-31	-25	2.11	ChiX	46	53	47	53	0.91	-8.16	-11.18	-0.864274	CAAAGAGG&CCUCUUUG	((((((((&))))))))	UAUAAAGGCAAGGGUGUUCGUUACGCCGACGAAGUCGUGCGUACCAAAGAGGCUAAGAAGAAGUAAGGUAACACUAUGGAUAAGAAAUCUGCUCGUAUCCGUCGUGCGACCCGCGCACGCCGCAAGCUCCAGGAGCUGGGCGCAACUCGC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0435477	0.8602904	rplR	947804	50S ribosomal subunit protein L18
b3413	53	67	59	65	6.52	ChiX	41	55	43	49	0.94	-9.41	-16.87	-0.996669	GUCAUUGGGGGAUUU&AAAUUCCUCUUUGAC	((((..(((((((((&)))))))))..))))	UUCCCCUGACCUUUGGUCUGCCACCAGAUGUUAUUCAUCCGCUAUUGUUCUCUUUUGACUUACAAGGAUGAACAUAUGCUAACAGUACCGGGAUUAUGCUGGCUAUGCCGAAUGCCACUGGCGUUAGGUCAUUGGGGGAUUUGUUCGGUC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0235542	0.8602904	yhgH	947915	DNA utilization protein YhgH
b3441	-16	-8	-14	-8	2.03	ChiX	45	53	45	51	0.91	-9.63	-12.57	-1.01997	CAAAGAGGA&UCCUCUUUG	(((((((((&)))))))))	CAAAAAAAUGCAUUUGACUCGCAUUUGAAAGUCAAUGAUGUUGAAAGGGACAUUUACCCCAAAGAGGACAAAGGAAUGAGUGAGAUAGUAAUACGCCACGCAGAAACACGGGAUUACGAGGCCAUCAGGCAGAUUCACGCCCAGCCGGAG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0211532	0.8602904	yhhY	947943	N-acetyltransferase YhhY
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

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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