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
b0333	51	74	56	62	2.7	MicC	6	28	17	23	4.89	-11.71	-19.3	-1.20697	AAAAUCUGUGGCACUUUCUGGCGU&AUGCCUUUAUUGUCACAGAUUUU	(((((((((((((.......((((&))))......)))))))))))))	AGGUCGGAUAAGACGCAUAGCGUCGCAUCCGACAACAAUCUCGACCCUACAAAUGAUAACAAUGACGAGGACAACAUGAGCGACACAACGAUCCUGCAAAACAGUACCCAUGUCAUUAAACCGAAAAAAUCUGUGGCACUUUCUGGCGUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0089209	0.9679271	prpC	947528	2-methylcitrate synthase
b3128	-16	6	-2	5	4.19	MicC	40	66	41	47	6.2	-12.58	-22.97	-1.29664	UGGAGAAUAUUGCACAAUGGCC&GGCCAUUGCAUUGCCACUGAUUUUCCA	((((((((...(((((((((((&))))))))...))).....))))))))	ACCCAAUGAAGUCAUUUAUUUUUAAAUGAGACCAGGUCCUCAUUUUAAUAACCCCUGGCUGGAGAAUAUUGCACAAUGGCCAACAUCGAAAUCAGACAAGAAACGCCAACUGCGUUUUAUAUAAAAGUUCACGACACAGAUAAUGUGGCA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0051283	0.853862	garD	947641	D-galactarate dehydrogenase
b3334	-68	-23	-51	-45	8.81	MicC	4	55	32	38	12.04	-9.85	-30.7	-1.01526	UGGCUUCCGAUGGAAAAAACAGAAAAAGAUCCGGUCAGUGGUGUAU&AUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCA	((((...((((((....((((((((((((((..(((((((((((((&)))))))...))))..)).)))))..)))))))))...))))))....))))	ACAGUCCUGGCUUCCGAUGGAAAAAACAGAAAAAGAUCCGGUCAGUGGUGUAUGGACAGUAAGGAACUCAGGGAAAUGAUUAAAUCAUGGUGGGCAGAAAAAUCCACAUCGGAAAAACAGAUCGUUGCGGCACUGGCGGUUCUCUCGCUC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0275399	0.9679271	gspM	947841	general secretory pathway component cryptic
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
b1140	-67	-42	-66	-60	5.94	MicC	44	68	61	67	4.39	-9.8	-20.13	-1.0101	GUUGGGGAGUUGGUAACACCUGUAAU&AUUGCAUUGCCACUGAUUUUCCAAC	((((((((((((((..((..((((((&)))))).))..))))))))))))))	CCGAGUUAGUUGGGGAGUUGGUAACACCUGUAAUCAAGAAAAAUGACUCAUUACUUUUGCAACGGAUUUUGAGUAAUGGCAGCCAGACCGCGUAAGAAUAAUGUUUCAGUCCCUAACUUAUAUCCGCUUUAUAGUAGGAAGGUAAAUAAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0283569	0.9679271	intE	948034	e14 prophage putative integrase
b3619	59	71	63	69	1.31	MicC	6	18	8	14	3.32	-9.81	-14.44	-1.01113	AUGAUAAAGGCAU&AUGCCUUUAUUGU	(((((((((((((&)))))))))))))	UUCGGAUGUGAUGGUAUGAUUACAGACAUUCGUGUCUGAGAUUGUCUCUGACUCCAUAAUUCGAAGGUUACAGUUAUGAUCAUCGUUACCGGCGGCGCGGGCUUUAUCGGCAGCAACAUCGUUAAAGCCCUGAAUGAUAAAGGCAUCACC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0281917	0.9679271	hldD	948134	ADP-L-glycero-D-mannoheptose-6-epimerase NAD(P)-binding
b3617	-16	4	-10	-4	4.14	MicC	47	69	58	64	4.31	-12.98	-21.43	-1.33787	UGUCUGGAGAAUCGCAAUGC&GCAUUGCCACUGAUUUUCCAACA	(((.((((((((((((((((&)))))))....))))))))))))	GUUAACGCGUUAUCUCGUCGCGACCUAUAAGUUUGGGUAAUAUGUGCUGGAAUUUGCCCUGUCUGGAGAAUCGCAAUGCGUGGAGAAUUUUAUCAGCAGUUAACCAACGAUCUGGAAACCGCACGGGCGGAAGGGUUGUUUAAAGAAGAG	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.003953	0.8150379	kbl	948138	glycine C-acetyltransferase
b3655	46	64	49	55	7.88	MicC	40	59	50	56	6.08	-11.06	-25.02	-1.13997	UUAGUGGCGAUCGCUGGCC&GGCCAUUGCAUUGCCACUGA	(((((((((((.((.((((&))))...)))))))))))))	UAACCAUUCCCGCCUUGAGGAUUGCGCGUAAAUCGUGCAUAACUCCCUUAUGUGCAUUUCACGGGAUGGAAGACCAUGAAAUUUAUUGGGAAGCUGCUUCUCUACAUUCUCAUCGCUCUGUUAGUGGCGAUCGCUGGCCUCUAUUUUCUU	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0133437	0.9679271	yicH	948171	putative inner membrane-anchored periplasmic AsmA family protein
b3673	-10	11	5	11	4.26	MicC	7	25	7	13	4.73	-9.9	-18.89	-1.02041	AUCCGUGAUAAUGAAAAGGCA&UGCCUUUAUUGUCACAGAU	(((.((((((((..(((((((&))))))))))))))).)))	GAUAGAUUCCUCUCCCGCAUUUAUGGGAAUGCGUAGUGACUUAUUCUAAUUAUUUUUAUAAAAGCAUCCGUGAUAAUGAAAAGGCAAAGAAACGUCAAUUUGUUAUUGAUGUUGGUAUUACUCGUGGCCGUCGGUCAGAUGGCGCAAACC	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0267449	0.9679271	emrD	948180	multidrug efflux system protein
b3690	16	45	16	22	13.63	MicC	32	56	50	56	9.02	-10.08	-32.73	-1.03896	GUGGCGAUUAUUGGCCUCGGCCCGGCAGGA&UUCUGUUGGGCCAUUGCAUUGCCAC	((((((((.....((...((((((((((((&))))))))))))...))))))))))	CCCGCCAUCAUACUUCACAAGGACUUCACUUUCAGACAAUAGUCUUUUGCCAUCGUGAUGAAUGUGAGUGAAAAGAUGGAACAUUUCGACGUGGCGAUUAUUGGCCUCGGCCCGGCAGGAUCGGCGUUGGCACGAAAGUUAGCAGGCAAA	GUUAUAUGCCUUUAUUGUCACAGAUUUUAUUUUCUGUUGGGCCAUUGCAUUGCCACUGAUUUUCCAACAUAUAAAAAGACAAGCCCGAACAGUCGUCCGGGCUUUUUUU	0.0240571	0.9679271	cbrA	948197	colicin M resistance protein FAD-binding protein putative oxidoreductase

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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