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
b1683	8	33	27	33	4.83	RyhB	38	66	38	44	3.3	-21.41	-29.54	-2.25121	GUAAUACUGAAGCAACUGACGAUGUC&GACAUUGCUCACAUUGCUUCCAGUAUUAC	(((((((((((((((.((((((((((&))))))).)))..)))))).)))))))))	GAUAUUCAAAUUUCACAACCCUAAAGCCCAGAAUGAAUGUGGCUGUGGCGAAAGCUUUGGGGUAUAGGCGGUACUAUGUCUCGUAAUACUGAAGCAACUGACGAUGUCAAAACCUGGACCGGCGGCCCGCUGAAUUAUAAAGAAGGAUUC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	4.71e-05	0.1636725	sufB	945753	component of SufBCD Fe-S cluster assembly scaffold
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
b3743	40	66	42	48	7.94	RyhB	34	60	52	58	6.76	-19.68	-34.38	-2.0693	CUGGAAGCAUUAAUGGGCAAUGCGCGC&GCACGACAUUGCUCACAUUGCUUCCAG	(((((((((....(((((((((((.((&)).)).)))))))))...)))))))))	AGCCUAACUCACUUUUGAUUCAUUAAAAAAGAAGGCUAAAAUAGAAUGAAUCAUCAAUCCGCAUAAGAAAAUCCUAUGGAAAAUUAUCUGAUCGACAAUCUGGACCGUGGCAUCCUGGAAGCAUUAAUGGGCAAUGCGCGCACCGCUUAC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0001586	0.1837117	asnC	948259	transcriptional activator of asnA autorepressor
b4255	-63	-43	-62	-56	5.2	RyhB	39	59	52	58	3.27	-18.09	-26.56	-1.90212	UGGAGGCAAUGUCAGUGGUGU&ACAUUGCUCACAUUGCUUCCA	((((((((((((.((((((((&)))))))).))))))))))))	UUGUCACAAAGGUGGAGGCAAUGUCAGUGGUGUGUGACAAUAAGAGUAUCGGCAGGACAUUAAGAGGAAUGAGCCAUGGCAAACCCGGAACAACUGGAAGAACAGCGUGAAGAAACACGUUUGAUUAUUGAAGAAUUACUGGAAGAUGGC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0004554	0.3956288	rraB	948773	protein inhibitor of RNase E
b2170	-33	-7	-33	-27	3.48	RyhB	2	24	18	24	7.69	-17.18	-28.35	-1.80643	CUCCGCGUCUUCCUCUUCCAGUGAUCG&CGAUCAGGAAGACCCUCGCGGAG	(((((((......((((((..((((((&))))))))))))....)))))))	UUUGAUUUCGCUGUCUGUUUAUUUUCUGACAAGCAGCGUAAACUCCGCGUCUUCCUCUUCCAGUGAUCGACCAGCAUGCAUAACUCCCCCGCAGUCUCCAGCGCGAAAUCGUUUGACCUGACCUCGACGGCGUUUUUAAUCGUUGCCUUU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0008131	0.5651045	setB	946673	lactose/glucose efflux system
b4019	-10	7	-1	6	4.63	RyhB	43	58	44	50	3.2	-16.82	-24.65	-1.76858	GGGAGCAAGUGUGAGCA&UGCUCACAUUGCUUCC	((((((((.((((((((&))))))))))))))))	UACCACAGAUGCGUUUAUGCCAGUAUGGUUUGUUGAAUUUUUAUUAAAUCUGGGUUGAGCGUGUCGGGAGCAAGUGUGAGCAGCAAAGUGGAACAACUGCGUGCGCAGUUAAAUGAACGUAUUCUGGUGCUGGACGGCGGUAUGGGCACC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.001018	0.5895917	metH	948522	homocysteine-N5-methyltetrahydrofolate transmethylase B12-dependent
b1181	49	69	60	66	3.61	RyhB	37	60	41	47	3.3	-16.27	-23.18	-1.71075	CUGGACGAAAUGAGCGAUGCG&CGACAUUGCUCACAUUGCUUCCAG	((((((((..(((((((((((&)).)))))))))..)))..)))))	ACUUUUUGCCGCCUGAAAGCGGCGGCAAAACUUGCAUCGCUGUGCCAGACUGGUUAUAAGGUGCGUUUUAACGUAAUGGCGGAACACCUGAUGAGCGAUGUACCUUUCUGGCAAAGUAAAACCCUGGACGAAAUGAGCGAUGCGGAAUGG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0014284	0.7090986	ycgN	945804	UPF0153 family cysteine cluster protein
b4348	-73	-53	-59	-53	7.54	RyhB	40	66	40	46	3.3	-15.87	-26.71	-1.66869	GUGAACUGGGGGCGAGCGAUG&CAUUGCUCACAUUGCUUCCAGUAUUAC	(((((((((((((((((((((&)))))))).....))))))))).))))	GCGUGAACUGGGGGCGAGCGAUGAGGCCGAUUUGCAGCGUCAGUUGCUGGAAGAAGCGUUUGGUGGGGUGAAGGAAUGAGUGCGGGGAAAUUGCCGGAGGGGUGGGUUAUCGCCCCAGUAUCUACGGUCACAACUCUAAUCCGAGGAGUA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0018209	0.7909534	hsdS	948867	specificity determinant for hsdM and hsdR
b3885	56	75	59	65	6.61	RyhB	41	62	53	59	3.3	-15.48	-25.39	-1.62768	UGCUGGGAGCCUGGAGCGAU&AUUGCUCACAUUGCUUCCAGUA	((((((((((.(((((((((&))))))).))..))))))))))	UUCAUACCUUGCCACAUAGCCAAACCCAUCCUUUCCCGCUACAGUUAAUUUCUUGUGGCGCGAAAGGAGGCAAAAAUGCUCUAUAUCUUUGAUUUAGGUAAUGUGAUUGUCGAUAUCGACUUUAACCGUGUGCUGGGAGCCUGGAGCGAU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0023007	0.8637808	yihX	948380	alpha-D-glucose-1-phosphate phosphatase anomer-specific
b0313	54	75	56	62	0.92	RyhB	40	61	53	59	3.3	-15.35	-19.57	-1.61401	ACUGGAAGCAAUAAAUGAAGUG&CAUUGCUCACAUUGCUUCCAGU	((((((((((((......((((&))))......))))))))))))	GACACAUUUUAUAUUGAACGUCCAAUCAAUAACCGCUUUAAUAGAUAAACACCGCUGAUGAAUGGAGUGGCGAAAAUGCCCAAAUUGGGGAUGCAGUCGAUCCGGCGCAGACAACUGAUCGACGCCACACUGGAAGCAAUAAAUGAAGUG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0024857	0.8637808	betI	944981	choline-inducible betIBA-betT divergent operon transcriptional repressor

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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