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
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
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
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
b1872	-14	-4	-12	-6	5.09	ChiX	44	54	46	52	0.93	-8.18	-14.2	-0.866392	UCAGGGAGGAA&UUCCUCUUUGA	(((((((((((&)))))))))))	UUAACGCGGUAUUUCCAGUACAACGCCAAAGAUAUUACCGAGAAACAGUGAUCCUCGUUGAUCAGGGAGGAAGUUAUGACAUUAACAAGACGUGAAUUUAUUAAACACAGCGGUAUUGCCGCUGGAGCGCUGGUGGUGACAUCGGCAGCA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0431199	0.8602904	torZ	946389	trimethylamine N-oxide reductase 2
b1957	31	40	34	40	4.82	ChiX	46	55	46	52	0.92	-8.08	-13.82	-0.855801	GUUAAAGAGG&CCUCUUUGAC	((((((((((&))))))))))	UCGCACUGGCUAUUAUGCAAAAUUCGCCAUCUUCAACUAAGGUGAACAAGUUUCACUCGAAAAAAGGAGGCGAGUAUGAGCUUUAUGGUUAGUGAGGAAGUUACGGUUAAAGAGGGCGGCCCGCGGAUGAUUGUCACUGGAUACUCCAGC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0453019	0.8602904	yodC	946466	protein YodC
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
b2019	-18	-7	-15	-9	3.01	ChiX	43	54	45	51	0.94	-10.86	-14.81	-1.15025	UUAAAGAGGAAU&AUUCCUCUUUGA	((((((((((((&))))))))))))	GGAAGAUCACCUUCCGGGGGCUUUUUUAUUGCGCGGUUGAUAACGGUUCAGACAGGUUUAAAGAGGAAUAACAAAAUGACAGACAACACUCGUUUACGCAUAGCUAUGCAGAAAUCCGGCCGUUUAAGUGAUGACUCACGCGAAUUGCUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0116502	0.8602904	hisG	946549	ATP phosphoribosyltransferase
b2098	-19	-6	-12	-6	0.4	ChiX	42	55	42	48	0.94	-9.74	-11.08	-1.03162	GUCAUGAAGGAAUU&AAUUCCUCUUUGAC	((((...(((((((&)))))))...))))	AAGGUAUUUAAAAGGUAUUAUUAAGUGGUAUUGUCAUCGCGUACCUUACAUUACCUGUCAUGAAGGAAUUAAAAGAUGAAAACAACAGCAAAGCUGUCGUUCAUGAUGUUUGUUGAAUGGUUUAUCUGGGGCGCGUGGUUUGUGCCAUUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0200479	0.8602904	yegT	946638	putative transporter YegT
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
b2216	-75	-60	-68	-62	2.37	ChiX	39	52	41	47	1.05	-8.35	-11.77	-0.884398	AGAGUCUGGAAUUUCA&UGAAAUUCCUCUUU	((((...(((((((((&))))))))).))))	AGAGUCUGGAAUUUCACACUGUACCCUUUAUACUGCCCUAUCACUUCGCGAAGUUUUAACAGGUCAUAAACACGAAUGCGUCAGAAAGAGACAACGGCCACGACCCGCUUUUCACUCCUACCGGGGAGCAUUACCCGCUUCUUUUUACUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0396511	0.8602904	rcsD	946717	RcsD phosphotransferase

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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