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
b1385	-3	20	12	18	5.43	MicC	1	21	3	9	4.41	-10.7	-20.54	-1.10287	GUGAUGACAGAGCCGCAUGUAGC&GUUAUAUGCCUUUAUUGUCAC	(((((((.((((..(((((((((&))))))))))))).)))))))	GUCACAGCGAAAAAAGUGACUUUUCUUGUCGCUGCGUACACUGAAAUCACACUGGGUAAAUAAUAAGGAAAAGUGAUGACAGAGCCGCAUGUAGCAGUAUUAAGCCAGGUCCAACAGUUUCUCGAUCGUCAACACGGUCUUUAUAUUGAU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0166105	0.9679271	feaB	945933	phenylacetaldehyde dehydrogenase
b4187	-2	10	-2	5	2.55	MicC	41	52	46	52	2.27	-9.78	-14.6	-1.00804	CAGUGCACUGGC&GCCAUUGCAUUG	(((((((.((((&)))).)))))))	UAGCAAUCUCUUUCUGUCAUGAAUCCAUGGCAGUGACCAUACUAAUGGUGACUGCCAUUGAUGGAGGGAGACACAGUGCACUGGCAAACUCACACCGUUUUUAAUCAACCUAUACCAUUAAAUAACAGCAACUUAUACCUGUCUGAUGGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.02869	0.9679271	aidB	948710	DNA alkylation damage repair protein flavin-containing DNA binding protein weak isovaleryl CoA dehydrogenase
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
b2920	2	18	9	15	3.47	MicC	51	66	53	59	2.9	-13.62	-19.99	-1.40384	UGGAAACUCAGUGGACA&UGCCACUGAUUUUCCA	((((((.(((((((.((&))))))))).))))))	AGGGAUGAACGCUUUCCUCGAAAAACGUAAACCUAAUUUCGUUGGUCAUUAAUCCCUGCGAACGAAGGAGUAAAAAUGGAAACUCAGUGGACAAGGAUGACCGCCAAUGAAGCGGCAGAAAUUAUCCAGCAUAACGACAUGGUGGCAUUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0025864	0.7974595	scpC	947402	propionyl-CoA:succinate CoA transferase
b1590	2	26	2	8	11.48	MicC	40	66	60	66	6.2	-10.74	-28.42	-1.10699	UGGGAAAUGGAUGGCAUGAGUGGCC&GGCCAUUGCAUUGCCACUGAUUUUCCA	((((((((...((((((((((((((&))))))).)).)))))...))))))))	UUAUCAAACCUAACGCCAACAGCCGCCCGACCGGCGAUACCACUGGUUAUCUGGCUAAUCCGGAGGAAGUGUAAAAUGGGAAAUGGAUGGCAUGAGUGGCCACUGGUUAUCUUUACCGUAUUGGGUCAAUGCGUAGUAGGCGCGCUGAUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0162135	0.9679271	ynfH	945822	oxidoreductase membrane subunit
b0633	2	18	9	15	6.88	MicC	39	55	42	48	4.76	-9.83	-21.47	-1.01319	UGCGUAAGCAGUGGCUC&GGGCCAUUGCAUUGCCA	((.((((((((((((((&)))))))))).))))))	UGGCUGGGUUCGGGAUUGUAAUGUCAAUCCACACCCACAGGAAAAUGUUGUCGAAAAGCGUGUAAGAGGUGCGCAAUGCGUAAGCAGUGGCUCGGGAUCUGCAUCGCGGCAGGAAUGCUCGCGGCAUGUACAAGCGAUGAUGGUCAGCAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.027864	0.9679271	rlpA	945241	septal ring protein suppressor of prc minor lipoprotein
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
b4327	3	12	5	11	1.53	MicC	89	98	90	96	4.56	-9.85	-15.94	-1.01526	GGAUGACUGU&ACAGUCGUCC	((((((((((&))))))))))	AAACGGCUUAAACGGUUGUCAGCCGCCCGAAUGGACGUAGAAUGCCCGCAAGGGCGGCUGACAGAGUAAAACGUAAUGGAUGACUGUGGUGCGAUUUUGCAUAAUAUUGAAACCAAAUGGCUUUAUGAUUUUCUGACCCUGGAAAAAUGC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0275399	0.9679271	hypT	948852	hypochlorite-responsive transcription factor
b2091	4	16	7	13	2.38	MicC	50	62	53	59	2.89	-10.87	-16.14	-1.12039	AAAUCAGUGGUGA&UUGCCACUGAUUU	(((((((((((((&)))))))))))))	ACAAGAGAAAGUCGUUCUCGCAGAAUAAUUUUUACCUGAGGGGGAGGUUAUCCCCCUUAACAAUCAGGAGUUUUUAUGAAAUCAGUGGUGAAUGAUACUGAUGGUAUCGUGCGCGUUGCAGAAAGCGUCAUUCCUGAAAUUAAACAUCAG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0149839	0.9679271	gatD	946598	galactitol-1-phosphate dehydrogenase Zn-dependent and NAD(P)-binding
b4496	8	31	19	25	7.77	MicC	39	64	47	53	6.64	-12.68	-27.09	-1.30695	GAAAAGUUCUGGCAAUGCUGGUCC&GGGCCAUUGCAUUGCCACUGAUUUUC	(((((....(((((((((((((((&))))))..)))))))))....)))))	UCCAAAUGUGCUUUUUUUUGGAUAACGGCACUUAUUGAUAUAUUCAUGAAGAUUAUAAUCACAAGGGAAUACAUAAUGAAAAGAAAAGUUCUGGCAAUGCUGGUCCCGGCGUUAUUAGUUGCUGGCGCAGCAAAUGCGGCUGAAGUCUAU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0048068	0.8384433	yedS	2847763	pseudogene outer membrane protein homology putative outer membrane protein

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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