Input and runtime details for job 6571257 (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 6571257 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:18:03 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:20:22 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:21:19 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:22:25 CET 2020
	Job Completed		@ Mon Jan 27 14:22:35 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

Description of the job

Spot42 - 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
b2659	-45	-24	-30	-24	6.31	Spot42	1	24	1	7	7.99	-10.83	-25.13	-1.11627	GAGCAUCGCCAUGUCACCCUAC&GUAGGGUACAGAGGUAAGAUGUUC	(((((((.((.(((.(((((((&))))))))))..))...)))))))	GUAGAUAUUUUUAGAUUAUGGCUACGAAAUGAGCAUCGCCAUGUCACCCUACAUCUCAUAAGAGGAUCGCUUCUGAUGAAUGCACUGACCGCCGUACAAAAUAACGCUGUCGAUUCAGGCCAGGACUAUAGCGGAUUCACCCUCACCCCG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0094499	0.9238006	csiD	948076	carbon starvation protein
b3664	17	32	17	23	7.49	Spot42	40	56	50	56	3.32	-10.58	-21.39	-1.0905	CCGAUUACGUGAGUAA&UUACUUCACGUAAUCGG	((((((((((((((((&)))).))))))))))))	AUAAUUAUCACUGAACCGUUGUUGUCAUUUGUUUUACAAAAGCAAGGGAUUAAAUCUCCUCCAAUGGACAAAAAAAUGAAUAAUGACAAUACCGAUUACGUGAGUAAUGAAUCAGGGACGCUUUCGCGAUUAUUUAAACUACCUCAGCAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0108957	0.9238006	adeQ	948174	adenine permease high affinity adenine:H+ symporter
b3685	-51	-36	-49	-43	4.25	Spot42	54	68	60	66	6.15	-11.08	-21.48	-1.14203	AUUCAGCCAUAAUCCG&CGGAUUUGGCUGAAU	(((((((((.((((((&)))))))))))))))	CUAUAAGGCAAAUCUGCUUCACCGAUUCAGCCAUAAUCCGUAGCAAUUAAAAUGUUAUCUCAAGAGAAAUGGACGAUGAGUGAUAUAGCAUUAACGGUCAGUAUUCUGGCUUUGGUGGCAGUCGUCGGUUUGUUUAUCGGCAACGUCAAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0081942	0.9238006	yidE	948193	putative transporter
b3690	-4	11	-2	5	3.57	Spot42	17	31	23	29	4.24	-9.42	-17.23	-0.970936	AAAGAUGGAACAUUU&AGAUGUUCUAUCUUU	(((((((((((((((&)))))))))))))))	CCCGCCAUCAUACUUCACAAGGACUUCACUUUCAGACAAUAGUCUUUUGCCAUCGUGAUGAAUGUGAGUGAAAAGAUGGAACAUUUCGACGUGGCGAUUAUUGGCCUCGGCCCGGCAGGAUCGGCGUUGGCACGAAAGUUAGCAGGCAAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0210242	0.9238006	cbrA	948197	colicin M resistance protein FAD-binding protein putative oxidoreductase
b3709	-53	-42	-48	-42	3.28	Spot42	1	13	1	7	5.11	-9.62	-18.01	-0.99155	CUCUUACCCUAC&GUAGGGUACAGAG	((((((((((((&)))))))).))))	GGCUAUAAGGAUGUUAGCCACUCUCUUACCCUACAUCCUCAAUAACAAAAAUAGCCUUCCUCUAAAGGUGGCAUCAUGACUGAUCAAGCUGAAAAAAAGCACUCUGCAUUUUGGGGUGUUAUGGUUAUAGCAGGUACAGUAAUUGGUGGA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0187797	0.9238006	tnaB	948220	tryptophan transporter of low affinity
b3827	60	68	60	66	1.66	Spot42	1	9	3	9	2.1	-9.16	-12.92	-0.944137	GUACCUUGC&GUAGGGUAC	(((((((((&)))))))))	UCGUUCUUUAUUUGGUCAGUUGUCAACCUGAUACUUCGCUACAAUGGAUACCCGUUAAUCAAAGAGUUUUCCAUUGUGGCGCUACUUAUCAUCACCACGAUUCUGUGGGCCUUCUCCUUUAGCUUUUAUGGCGAGUACCUUGCGGGGCAC	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0243401	0.9238006	yigM	948309	putative inner membrane EamA-like transporter
b3816	-71	-41	-47	-41	5.45	Spot42	4	37	4	10	11.32	-10.38	-27.15	-1.06988	GGUCUGAAACCCAAUUUGUUUCUGUGUGCCC&GGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACC	(((((((((....((((....((.(((((((&))))))).))...))))........)))))))))	UAAUGGUCUGAAACCCAAUUUGUUUCUGUGUGCCCACCGAACUGUCCGAUAUUUUAAGCAUUGGGAGUCCCGGUCAUGCUGAGCGCAUUUCAACUGGAAAAUAACCGACUGACCCGGCUGGAAGUCGAAGAGUCACAACCCCUUGUAAAU	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.012208	0.9238006	corA	948351	magnesium/nickel/cobalt transporter
b3878	60	67	61	67	0.85	Spot42	1	8	1	7	2.09	-10.22	-13.16	-1.05339	UACCCUAC&GUAGGGUA	((((((((&))))))))	UAUGAGAAUCAUUUUACAUAAGCCUGUAAUAACAGGAAGGCAACAAUCUCGUUCUCAACUCUAUGGAGAUUAGUUAUGGAUACGCCACGUCCACAGUUAUUAGAUUUUCAAUUUCAUCAGAAUAACGACAGUUUUACCCUACAUUUUCAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0133694	0.9238006	yihQ	948376	putative sulpholipid alpha-glucosidase alpha-glucosyl fluoride glucosidase
b3908	-12	16	10	16	4.66	Spot42	1	34	1	7	9.12	-9.96	-23.74	-1.02659	CUGGAGAUGAAUAUGAGCUAUACCCUGC&GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAG	((((((((((((((...((.((((((((&)))))))).)).......)))))).))).)))))	CAUUUAAUUAACUAUAAUGAACCAACUGCUUACGCGGCAUUAACAAUCGGCCGCCCGACAAUACUGGAGAUGAAUAUGAGCUAUACCCUGCCAUCCCUGCCGUAUGCUUACGAUGCCCUGGAACCGCACUUCGAUAAGCAGACCAUGGAA	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0154934	0.9238006	sodA	948403	superoxide dismutase Mn
b3921	-74	-67	-73	-67	0.43	Spot42	50	57	50	56	0.29	-9.55	-10.27	-0.984335	UCCGAUUA&UAAUCGGA	((((((((&))))))))	CUCCGAUUAAAACGAUAUCUGUCGCCCUUGUCAAAAGGGUAGAAUCCUGGAAAAGACAACCAUCAAGGAACUUACAUGACCAUACAGCAAUGGUUAUUCUCAUUUAAAGGGCGUAUUGGACGCCGUGAUUUCUGGAUUUGGAUAGGCCUG	GUAGGGUACAGAGGUAAGAUGUUCUAUCUUUCAGACCUUUUACUUCACGUAAUCGGAUUUGGCUGAAUAUUUUAGCCGCCCCAGUCAGUAAUGACUGGGGCGUUUUUUA	0.0195371	0.9238006	yiiR	948417	DUF805 family putative inner 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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