Input and runtime details for job 8403881 (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 8403881 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:15:25 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:18:18 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:19:13 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:20:45 CET 2020
	Job Completed		@ Mon Jan 27 14:20:57 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8403881&toolName=IntaRNA ( 30 days expiry )

Description of the job

RyhB - 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
b0728	-74	-59	-66	-60	1.61	RyhB	50	64	51	57	2.98	-10.97	-15.56	-1.15347	AAUGCCCGGAAGCGAU&AUUGCUUCCAGUAUU	(((((..(((((((((&))))))))).)))))	CAAUGCCCGGAAGCGAUACGAAAUAUUCGGUCUACGGUUUAAAAGAUAACGAUUACUGAAGGAUGGACAGAACACAUGAACUUACAUGAAUAUCAGGCAAAACAACUUUUUGCCCGCUAUGGCUUACCAGCACCGGUGGGUUAUGCCUGU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0284439	0.9496255	sucC	945312	succinyl-CoA synthetase beta subunit
b0892	-18	15	1	7	10.86	RyhB	37	66	43	49	3.3	-11.3	-25.46	-1.18817	GUAAGUAGAGGCACCUGAGUGAGCAAUCUGUCG&CGACAUUGCUCACAUUGCUUCCAGUAUUAC	((((...((((((.....(((((((((..((((&)))))))))))))..)))))).....))))	UGGAUGCAGCGAAAUUUACCUUCACCCCGCCGCAAGGCGUCACGGUAGAUGAUCAACGUAAGUAGAGGCACCUGAGUGAGCAAUCUGUCGCUCGAUUUUUCGGAUAAUACUUUUCAACCUCUGGCCGCGCGUAUGCGGCCAGAAAAUUUA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0239401	0.9496255	rarA	945505	recombination intermediate processing DNA-dependent ATPase
b0894	-38	-18	-24	-18	3.25	RyhB	43	62	43	49	3.3	-19.93	-26.48	-2.09559	UACUGGAAUCAAUCGUGAGCA&UGCUCACAUUGCUUCCAGUA	((((((((.((((.(((((((&))))))))))).))))))))	CGAACUGCUAUAGAAAUAAUUACACAAUACGGUUUGUUACUGGAAUCAAUCGUGAGCAAGCUUGAGUGAGCCAUUAUGAAAACGAAAAUCCCUGAUGCGGUAUUGGCUGCUGAGGUGAGUCGCCGUGGUUUGGUAAAAACGACAGCGAUC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0001337	0.1837117	dmsA	945508	dimethyl sulfoxide reductase anaerobic subunit A
b0896	51	69	52	58	3.7	RyhB	36	54	47	53	3.22	-12.7	-19.62	-1.33537	GCAAUGUGUAGCAGGUGGU&ACGACAUUGCUCACAUUGC	((((((((.((((.((.((&)).))..))))))))))))	UGAUCAAACCCAAUGCCAAUAGCCGCCCGACCGGGGAUACCACUGGCUAUCUGGCAAACCCGAAGGAGGUGUGAGAUGGGAAGUGGAUGGCAUGAAUGGCCGCUGAUGAUCUUCACGGUCUUCGGGCAAUGUGUAGCAGGUGGUUUUAUC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.011288	0.9496255	dmsC	945502	dimethyl sulfoxide reductase anaerobic subunit C
b0943	-22	6	-5	2	6.9	RyhB	37	60	41	47	3.3	-12.08	-22.28	-1.27018	CUGGUUUACCAGUGAAGGAGUGAUGUUG&CGACAUUGCUCACAUUGCUUCCAG	((((.....(((((...(((((((((((&))))))))))).)))))...))))	CCACAAAGGCGGGAGCAACGGGCGGUAAUGCGACGGCGGUUCUCUAUUUUGAUCUGGUUUACCAGUGAAGGAGUGAUGUUGAAACGGAUAAUCUGGAUUCUGUUCUUAUUGGGAUUAACGUGGGGCUGUGAGCUAUUUGCCCAUGAUGGC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0158115	0.9496255	ycbV	945562	putative fimbrial-like adhesin protein
b0968	-11	6	-2	5	3.42	RyhB	37	58	38	44	3.22	-13.79	-20.43	-1.44998	GGAGAGCAGCAAUGUCG&CGACAUUGCUCACAUUGCUUCC	(((.(((((((((((((&)))))))))......)))))))	GCAAAGAAAUGGGCGUCAUUGUCCGGAGUUUUCCAUGGAUUUGCAACGCGUCCAUUAAGGAUAAGGAGAGCAGCAAUGUCGAAAGUCUGCAUAAUUGCCUGGGUUUACGGGCGAGUUCAGGGCGUAGGAUUUCGCUACACCACACAGUAC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0061458	0.9291058	yccX	945304	weak acylphosphatase
b1013	-75	-34	-47	-41	10.22	RyhB	7	44	14	20	13	-12.26	-35.48	-1.28911	CGAUGAGAGUGCAGAAGGUCGAGGCCGGGCGGGGGUUUUGCU&AGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUG	(((((...((((...((((.....((..(((((((((((.((&)).)))))))))))))...))))....))))..)))))	CGAUGAGAGUGCAGAAGGUCGAGGCCGGGCGGGGGUUUUGCUAUCCUGUUGCCAAUCUACAAGAGGGGAGAGCGCAUGACGCAAGGCGCAGUGAAAACAACGGGUAAACGUUCGCGCGCAGUAAGCGCGAAGAAAAAAGCGAUUCUUAGC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0143473	0.9496255	rutR	945075	rut operon transcriptional repressor for
b1044	63	73	66	72	2.88	RyhB	52	62	53	59	2.88	-12.49	-18.25	-1.31329	UGCUGGAAGCA&UGCUUCCAGUA	(((((((((((&)))))))))))	GCUGCGAAUCAGCCAACCUGAAAGUAUGGAUAACACAACCCUCAAGGAUGACUAAUCAUUGAGGAAAUAGAAUAAAUGUUCAGACCUUUUUUAAACUCUCUUAUGCUCGGCAGUUUGUUUUUUCCUUUUAUUGCCAUUGCUGGAAGCACC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.012662	0.9496255	ymdA	949012	uncharacterized protein
b1107	-41	18	-41	-35	17.57	RyhB	37	81	75	81	14.89	-13.54	-46	-1.4237	CACCUGGCGGCAGCUAUUAAUAAAACAAUAAGGAGAGCAGUGUGGGUCCAGUAAUGUUG&CGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUG	((((((((....((((.(((((.........(((.(((((((((.....((((((((((&))))))))))))))))))))))..)))))..))))..))))))))	CCGGCGAUCAACAAUUUAUCAGGCUGGCCGAUGACACCUGGCGGCAGCUAUUAAUAAAACAAUAAGGAGAGCAGUGUGGGUCCAGUAAUGUUGGAUGUCGAAGGUUACGAACUGGACGCGGAAGAGCGUGAAAUACUGGCGCAUCCGCUG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0070778	0.9291058	nagZ	945671	beta N-acetyl-glucosaminidase
b1120	-17	5	-7	-1	9.07	RyhB	46	68	52	58	3.24	-14.88	-27.19	-1.5646	AAGUGGUGCCGGAAGCAAUGGA&UCACAUUGCUUCCAGUAUUACUU	(((((((((.((((((((((((&)).)))))))))).)))))))))	CGUAAAAAUAAACGCCGCCUGCGCGAGCGUUUGCGUCAGCGUAUUUUUUUCAGAGAUAAAGUGGUGCCGGAAGCAAUGGAAAAACCAAGAGUACUCGUACUGACAGGGGCAGGAAUUUCUGCGGAAUCAGGUAUUCGUACCUUUCGCGCC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0032796	0.9291058	cobB	945687	deacetylase of acs and cheY chemotaxis 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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