Input and runtime details for job 4596356 (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 4596356 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:10:48 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:13:48 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:14:50 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:16:49 CET 2020
	Job Completed		@ Mon Jan 27 14:17:02 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4596356&toolName=IntaRNA ( 30 days expiry )

Description of the job

FnrS - 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
b0642	-72	-63	-71	-65	2.78	FnrS	68	77	70	76	1.76	-10.63	-15.17	-1.08307	UGCUAUGCGG&CUGCAUAGCA	((((((((((&))))))))))	CUAUGCUAUGCGGAUCUGAAAAACCACCUCAACGCUACAUUUGUAGCCGUAUUGAAAACAGGACCACUGGCUGCCAUGCAAGAGCAAUACCGCCCGGAAGAGAUAGAAUCCAAAGUACAGCUUCAUUGGGAUGAGAAGCGCACAUUUGAA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.017071	0.9422174	leuS	947497	leucyl-tRNA synthetase
b1049	3	41	6	12	14.57	FnrS	21	54	44	50	13.61	-10.56	-38.74	-1.07594	GAAUAAGACAACUGAGUACAUUGACGCAAUGCCCAUCGC&GCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUC	(((((((((((..(((........(((((((((((((((&))))))))))))))))))....)))))))).)))	CCACUGAAAUGCGUGCUGCGCUGGUGAAUGCCGAUCAGACGUUGAGUGAAACCUGGAGCUACCAGUUACCUGCCAAUGAAUAAGACAACUGAGUACAUUGACGCAAUGCCCAUCGCCGCAAGCGAGAAAGCGGCAUUGCCGAAGACUGAU	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0178846	0.9422174	opgH	945624	OPG biosynthetic ACP-dependent transmembrane UDP-glucose beta-12 glycosyltransferase nutrient-dependent cell size regulator FtsZ assembly antagonist
b3306	-14	6	-14	-8	4.69	FnrS	35	55	49	55	4.12	-10.56	-19.37	-1.07594	GGGAGUAAAGACAGAUGAGC&GCUCCAUAUUGUCUUACUUCC	((((((((.((((.((((((&)))).))..))))))))))))	AUGCGCGGUGAAAUCCCGGGUCUGAAAAAGGCUAGCUGGUAAUUGUCACCAAUUGAAUCACGGGAGUAAAGACAGAUGAGCAUGCAAGAUCCGAUCGCGGAUAUGCUGACCCGUAUCCGUAACGGUCAGGCCGCGAACAAAGCUGCGGUC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0178846	0.9422174	rpsH	947802	30S ribosomal subunit protein S8
b1266	10	29	16	22	5.17	FnrS	61	89	68	74	4.63	-10.53	-20.33	-1.07289	ACGAAUUAUGCAGUGAUUUA&UGAAUUACUGCAUAGCACAAUUGAUUCGU	((((((((((((((((((((&)))))))))))))).........))))))	CAGCUCAUUUCAGAAUAUUUGCCAGAACCGUUAUGAUGUCGGCGCAAAAAACAUUAUCCAGAACGGGAGUGCGCCUUGAGCGACACGAAUUAUGCAGUGAUUUACGACCUGCACAGCCAUACCACAGCUUCCGAUGGCUGCCUGACGCCA	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0182438	0.9422174	yciV	945857	PHP domain protein
b4648	-45	-29	-42	-36	6.03	FnrS	60	76	67	73	3.49	-10.5	-20.02	-1.06983	GUUAUGCAGUGACUCGA&UUGAAUUACUGCAUAGC	((((((((((((.((((&)))).))))))))))))	CGUAAAUGGCGCAUCGGCGGGCAGCAACAGGUUAUGCAGUGACUCGACGUUGUCGGCCUGCUCCAUGCAAUACGGUUUAAUGACGUUGGCUAUUUCCGGCAGAUUUUUCAGAAACAUACUGGUUUAACGCCAGCAGCGUGGAAGCGGCGU	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0186096	0.9422174	ysaC	5625574	pseudogene
b2019	28	36	28	34	3.04	FnrS	68	76	70	76	1.75	-10.49	-15.28	-1.06881	GCUAUGCAG&CUGCAUAGC	(((((((((&)))))))))	GGAAGAUCACCUUCCGGGGGCUUUUUUAUUGCGCGGUUGAUAACGGUUCAGACAGGUUUAAAGAGGAAUAACAAAAUGACAGACAACACUCGUUUACGCAUAGCUAUGCAGAAAUCCGGCCGUUUAAGUGAUGACUCACGCGAAUUGCUG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.018733	0.9422174	hisG	946549	ATP phosphoribosyltransferase
b0353	-31	-22	-28	-22	3.34	FnrS	1	10	1	7	2.78	-10.49	-16.61	-1.06881	AUUCACCUGC&GCAGGUGAAU	((((((((((&))))))))))	CAUUAAAUAGUUCUGAUUACGCGGCUGGCAAUGUAUCAGUCGCGAUUCACCUGCACUCGCAACGAGGUUCAUCUUAUGUCGACUCGUACCCCUUCAUCAUCUUCAUCCCGCCUGAUGCUGACCAUCGGGCUUUGUUUUUUGGUCGCUCUG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.018733	0.9422174	mhpT	944997	3-hydroxyphenylpropionic transporter
b1206	-51	-43	-49	-43	2.01	FnrS	1	9	1	7	2.36	-10.45	-14.82	-1.06473	UUCACCUGC&GCAGGUGAA	(((((((((&)))))))))	UCCAUUUGUAUGACCUAUGCCUCCUUCACCUGCCAUUUAGUUGACAGAUGAUGCGCUCACGGAUGAAACAUUAUUGUGAACAAAAUAUUUUCCUCACAUGUGAUGCCUUUCCGCGCUCUGAUCGACGCUUGCUGGAAAGAAAAAUAUACU	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.019234	0.9422174	dauA	945770	C4-dicarboxylic acid transporter
b4141	-71	-55	-61	-55	6.59	FnrS	73	88	73	79	2.24	-10.44	-19.27	-1.06372	CGAAUCUGAUUGUGCUA&UAGCACAAUUGAUUCG	((((((..(((((((((&))))))))).))))))	UAAGCGAAUCUGAUUGUGCUACCAUCGAAAAUCUACGCAGUUGCCCAAAAUUUGGGCGCAAUCGGACAUCAACCCAUGAGUGGACUCAAACAAGAACUGGGGCUGGCCCAGGGCAUUGGCCUGCUAUCGACGUCAUUAUUAGGCACUGGC	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0193611	0.9422174	yjeH	948656	putative transporter
b1526	-16	3	-4	3	5.88	FnrS	71	89	71	77	4.45	-10.44	-20.77	-1.06372	ACGAAUCGAGAAUGCUAUG&CAUAGCACAAUUGAUUCGU	(((((((((...(((((((&)))))))...)))))))))	GUAUGAAGAUACGCAGAUUUACUCUUGCUUUAAAAUGAAUAAUAUUAAGCCACUUAUUCACGAAUCGAGAAUGCUAUGGAUCUGACCCAACUGGAGAUGUUCAACGCGGUUGCCGAAGCUGGCAGCAUAACCCAGGCUGCAGCAAAAGUG	GCAGGUGAAUGCAACGUCAAGCGAUGGGCGUUGCGCUCCAUAUUGUCUUACUUCCUUUUUUGAAUUACUGCAUAGCACAAUUGAUUCGUACGACGCCGACUUUGAUGAGUCGGCUUUUUUUU	0.0193611	0.9422174	yneJ	946079	putative DNA-binding transcriptional regulator

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 3.1.3 linking Vienna RNA package 2.4.14

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