Input and runtime details for job 1972078 (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 1972078 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:13:56 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:16:07 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:17:05 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:18:21 CET 2020
	Job Completed		@ Mon Jan 27 14:18:31 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1972078&toolName=IntaRNA ( 30 days expiry )

Description of the job

MicC - 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
b3354	1	75	12	18	11.83	MicC	8	70	50	56	12.15	-10.9	-34.88	-1.12348	AUGUUGAUUCCGUGGCAAGACCUCUCCCCCGAAACGCUGGAAAAUUUAAUUGAAAGCUUUGUGUUACGUGAAGGC&GCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAU	((((((..((.(((((((.........(((((......(((((.......(((((..((((((.....(((((((&)))))))....))))))))))))))))..)))))........))))))).)).....))))))	UACAUUACUUCAUCCGCAAAUGUGGCUGGAGUCACGCAUUCCUGACUGGUUAACAACGUAUCUGGAGGCGAAAUCAUGUUGAUUCCGUGGCAAGACCUCUCCCCCGAAACGCUGGAAAAUUUAAUUGAAAGCUUUGUGUUACGUGAAGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0147129	0.9679271	yheU	947863	UPF0270 family protein
b1456	57	69	58	64	4.24	MicC	8	20	13	19	3.98	-10.52	-18.74	-1.08431	UGACGAUAAAGGC&GCCUUUAUUGUCA	(((((((((((((&)))))))))))))	AAAAUCCCAGACUAAAUCAUCACAUAACCAUGACAUUUUUCUGAUAUUCCCCGGUAACGCCAGAUGUCGACUCGCUUAACCACCCUCAGCCAUACCAGUGAAGGCCACCGCGUGUCGGUCCACUACGGCUAUGACGAUAAAGGCCGCCUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0185126	0.9679271	rhsE	946026	pseudogene Rhs family
b1776	-72	8	-60	-54	13.29	MicC	8	70	57	63	12.15	-10.51	-35.95	-1.08328	AUGUUGACCUCAAAAAUCAUGUGGGUAAGUAUGAUGGCCAUCUAAGCAAAACUAAACACAGAGGAUGACGCAAUGAAAGC&GCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAU	((((((......(((((((.(((.(((((((..((((((.......((.........(((((((((((..(((((((.((&)).))))))).........)))))))))))))))))))))).)))))))))))))).))))))	UUAAUGUUGACCUCAAAAAUCAUGUGGGUAAGUAUGAUGGCCAUCUAAGCAAAACUAAACACAGAGGAUGACGCAAUGAAAGCACUGGCUCGGUUUGGCAAGGCCUUUGGCGGCUACAAGAUGAUUGAUGUCCCACAACCCAUGUGUGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.018624	0.9679271	ydjL	946299	putative Zn-dependent NAD(P)-binding oxidoreductase
b2771	-18	-8	-14	-8	0.99	MicC	9	19	9	15	0.94	-11.47	-13.4	-1.18223	GACAAUGAAGG&CCUUUAUUGUC	(((((((((((&)))))))))))	GCGAUGACGGGGCGUUGCCUUUUCGGCUUCUCAGGCGAGAAGCCGUUCUUAUUACCGGACAAUGAAGGGGUAAAGAUGAACACUUCACCGGUGCGAAUGGAUGAUUUACCGCUUAACCGUUUUCACUGCCGCAUUGCUGCGCUCACUUUC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0103621	0.9679271	ygcS	947238	putative MFS sugar transporter membrane protein
b1817	-20	-10	-16	-10	0.62	MicC	9	19	9	15	0.94	-9.88	-11.44	-1.01835	GAUAAUAAAGG&CCUUUAUUGUC	(((((((((((&)))))))))))	CGAUUCGAUUGUGGACGACGAUUCAAAAAUACAUCUGGCACGUUGAGGUGUUAACGAUAAUAAAGGAGGUAGCAAGUGACCAUUGCUAUUGUUAUAGGCACACAUGGUUGGGCUGCAGAGCAGUUGCUUAAAACGGCAGAAAUGCUGUUA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0270603	0.9679271	manX	946334	fused mannose-specific PTS enzymes: IIA component/IIB component
b4535	31	66	31	37	17.22	MicC	17	66	60	66	11.11	-13.33	-41.66	-1.37395	UGGAAGAUGGUGGUGGUGCUACUGGCAAUCUGUGGC&GUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCA	((((((((.((((((((((...((((((((((((((&))))))))))..............))))..))))))))))..))))))))	AACAAAAAAUCCCUUGAUGCCUGUCCCUUUUGUUACACUCCGUUAUCACGCACAAGAGAUAUGCAGGACACUGGUAUGCCGACUAAACGCUUUGAUAAAAAACACUGGAAGAUGGUGGUGGUGCUACUGGCAAUCUGUGGCGCUAUGUUG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0031383	0.7974595	yniD	1450269	uncharacterized protein
b0982	-12	18	1	7	4.13	MicC	22	56	39	45	9.06	-11.1	-24.29	-1.1441	GUGGAUUCAAACAUGGCCCAACUAAAAUUU&AGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCAC	((((........((((((((((((((((((&))))))))......)))))))))).......))))	CCGUGUGAUUUCUCUGCUGGUACCGACGAUUUCCGGGGUGCAUGACCUGACAGAGACUUCACGGUGGAUUCAAACAUGGCCCAACUAAAAUUUAACUCAAUCCUGGUGGUUUGUACCGGCAACAUUUGCCGUUCGCCCAUUGGCGAGCGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0130207	0.9679271	etp	945236	O-antigen capsule forming protein-tyrosine-phosphatase Etk-P dephosphorylase
b4271	-9	24	-2	5	7.14	MicC	23	54	41	47	9.06	-10.7	-26.9	-1.10287	GGGAAUACGAUGGCAUUAACAGAUAUCAAAGUC&GAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCC	((.(((.(((((((...((((((....((((((&))))))....))))))..))))))).))).))	AUCUACCAACAUAUGUUGGUACAGAUGAUGGUAUUUCCGGUUCGAUAAUGCUUGUACCAACAGGGAGGGAAUACGAUGGCAUUAACAGAUAUCAAAGUCAGAGCAGCCAAGCCAACGGAUAAGCAAUAUUAGCUGACUGAUGGUGGCGGU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0166105	0.9679271	intB	948782	pseudogene integrase homologyIS phage Tn Phage-related functions and prophages KpLE2 phage-like element P4-like integrase
b0642	3	35	26	32	5.71	MicC	23	53	26	32	9.06	-10.52	-25.29	-1.08431	GCAAGAGCAAUACCGCCCGGAAGAGAUAGAAUC&GAUUUUAUUUUCUGUUGGGCCAUUGCAUUGC	((((..(((((...((((...((((((((((((&)))))))))).))...)))).))))).))))	CUAUGCUAUGCGGAUCUGAAAAACCACCUCAACGCUACAUUUGUAGCCGUAUUGAAAACAGGACCACUGGCUGCCAUGCAAGAGCAAUACCGCCCGGAAGAGAUAGAAUCCAAAGUACAGCUUCAUUGGGAUGAGAAGCGCACAUUUGAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0185126	0.9679271	leuS	947497	leucyl-tRNA synthetase
b2247	42	62	44	50	6.63	MicC	30	55	47	53	8.97	-10.24	-25.84	-1.05545	UGGCGGUGCGACAGCAGAAAA&UUUUCUGUUGGGCCAUUGCAUUGCCA	(((((((((((((((((((((&)))))))))).....)))))))))))	CGCCAGGGAUAUUUCACGUCUGUUGGGAUGGAAAAGUCCCUUUGACUUACAAGCCUCAUAACAAUGGAGAACAUCAUGACCCUACCAAAAAUUAAACAGGUUCGCGCCUGGUUUACUGGCGGUGCGACAGCAGAAAAAGGCGCUGGCGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.021882	0.9679271	rhmD	945881	L-rhamnonate dehydratase

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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