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
b0156	-11	13	3	9	5.27	RyhB	37	59	41	47	3.29	-11.5	-20.06	-1.2092	UGGAGCAAAAUAUGAGUGAUGACG&CGACAUUGCUCACAUUGCUUCCA	((((((((....(((((((((.((&)).)))))))))..)))).))))	UACCAGGGUAUUAGAUAAUGGCGAUUAUUAUUGGGUUAGAAUUUGCCCAAUUGCCGAUGUCGUUUGGAGCAAAAUAUGAGUGAUGACGUAGCACUGCCGCUGGAGUUUACCGACGCAGCAGCCAACAAAGUUAAAAGCCUGAUCGCUGAC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0215456	0.9496255	erpA	944857	iron-sulfur cluster insertion protein
b3391	-11	13	5	11	0.42	RyhB	46	68	49	55	3.24	-11.42	-15.08	-1.20079	AGGAGAUACAAAUGAAGCAAUGGA&UCACAUUGCUUCCAGUAUUACUU	(((..((((....(((((((((((&)).)))))))))..))))..)))	CAGACGUACUAACGCUGGGUACCGGGACAAACUGCGAACCGCCACAAUGGUUGUGGCAACGGCAAGGAGAUACAAAUGAAGCAAUGGAUAGCCGCACUACUGUUGAUGCUGAUACCCGGCGUACAGGCGGCAAAGCCGCAAAAAGUGACG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0224751	0.9496255	hofQ	947901	DNA catabolic putative fimbrial transporter
b3777	15	47	35	41	9.19	RyhB	51	84	56	62	14.45	-11.41	-35.05	-1.19973	CAGCCCUAAGGUUGGUGAAAUACUGGAAUGCAA&UUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUG	((((((...(((((((((((((((((((.((((&))))))))))))))..))).)))))).)).))))	CAUUAGACUUAGAAAAUAUCGGGUCGUAACGUUGUGUUAUUACUUUUUCAGAGUUUACUAAGGAGAGGUUUACUCGUGGCGAUUAAUUUCAGCCCUAAGGUUGGUGAAAUACUGGAAUGCAACUUUGGUAACUAUCCUGUUAGCCAAAAU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0225939	0.9496255	yifN	2847676	PemK toxin family pseudogene
b2211	-12	13	7	13	8.49	RyhB	6	30	6	12	10.22	-11.41	-30.12	-1.19973	CGGGUUUUCUGCAUGGAACUUCUUG&CAGGAAGACCCUCGCGGAGAACCUG	((((((((((((..((..(((((((&)))))))..))..))))))))))))	AAAUAAGAAUUAUUAUUGCUGUGCGCGCGAAGAUGUUUAAACUGCGGGCUGUAAUUCAUUGUCCGGGUUUUCUGCAUGGAACUUCUUGUACUUGUCUGGCGGCAGUAUCGCUGGCCAUUUAUCAGUGUGAUGGCGCUAAGCCUCGCCAGU	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0225939	0.9496255	yojI	946705	microcin J25 efflux ABC transporter permease/ATPase
b2155	-55	-41	-50	-44	3.08	RyhB	41	57	44	50	3.2	-11.36	-17.64	-1.19448	GAAGAUGUGAGCGAU&AUUGCUCACAUUGCUUC	(((((((((((((((&)))))))))))..))))	CGUACGCAAGGGGACGUGAAGAAGAUGUGAGCGAUAACCCAUUUUAUUUUCGUAGUUACCUCAUGGAGAUAUGGAAUGUUUAGGUUGAACCCUUUCGUACGGGUCGGGCUGUGUUUGUCCGCUAUUUCUUGUGCAUGGCCUGUGUUAGCG	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0231967	0.9496255	cirA	949042	colicin IA outer membrane receptor and translocator ferric iron-catecholate transporter
b3835	-35	-4	-23	-17	9.16	RyhB	53	86	71	77	14.49	-11.36	-35.01	-1.19448	GCCCUGACCAAACGGCUGGAAAAACUGGAGGC&GCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGC	(((...(((...(((((((..(((((((((((&))))))))).....))..))))))))))...)))	GUUUGCGGAAGAGACGGCUGCCGUCGAGCGUGCUGUUGAUGCCCUGACCAAACGGCUGGAAAAACUGGAGGCUAAAUGACGCCAGGUGAAGUACGGCGCCUAUAUUUCAUCAUUCGCACUUUUUUAAGCUACGGACUUGAUGAACUGAUC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0231967	0.9496255	ubiB	948322	regulator of octaprenylphenol hydroxylation ubiquinone synthesis regulator of 2'-N-acetyltransferase putative ABC1 family protein kinase
b3311	-68	-41	-49	-43	11.36	RyhB	37	60	39	45	3.3	-11.34	-26	-1.19237	CUGUUGAAGCAAGUGCGUCGCGAUGUCG&CGACAUUGCUCACAUUGCUUCCAG	(((..((((((((((....(((((((((&))))))))).))).))))))))))	GUCUCACCUGUUGAAGCAAGUGCGUCGCGAUGUCGCACGCGUUAAGACUUUACUGAACGAGAAGGCGGGUGCGUAAUGACCGAUAAAAUCCGUACUCUGCAAGGUCGCGUUGUUAGCGACAAAAUGGAGAAAUCCAUUGUUGUUGCUAUC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0234421	0.9496255	rpsQ	947808	30S ribosomal subunit protein S17
b4516	-39	-2	-9	-3	8.43	RyhB	21	62	22	28	7.99	-11.31	-27.73	-1.18922	UACUGAUUUAGUGUAUGAUGGUGUUUUUGAGGUUCUCC&GGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUA	(((((....((((((((...(((((((..(((((((((&))))))))).)))))))..))).....))))).....)))))	UUCAUCGCAUGGACAAUACGGGUGAUGCUGCCAACUUACUGAUUUAGUGUAUGAUGGUGUUUUUGAGGUUCUCCAGUGGCUUCUGUUUCUAUCAGCUGUCCCUCCUGUUCAGCUACUGACGGGGUGGUGCGUAACGGCAAAAGCACUGCC	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0238147	0.9496255	insA	1450250	IS1 repressor TnpA
b3645	-7	3	-7	-1	3.42	RyhB	40	49	43	49	1.15	-11.31	-15.88	-1.18922	GUGGGCAAUG&CAUUGCUCAC	((((((((((&))))))))))	UGAGAUACUCACAACUGUAUAUAAAUACAGUUACAGAUUUACUUUCUUUGCAAUUGAUAUCACAUGGAGUGGGCAAUGAACGAACAUCAUCAACCUUUUGAAGAGAUAAAACUGAUUAAUGCAAACGGAGCAGAACAAUGGUCAGCAAGA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0238147	0.9496255	dinD	948153	DNA damage-inducible protein
b0892	-18	15	1	7	10.86	RyhB	37	66	43	49	3.3	-11.3	-25.46	-1.18817	GUAAGUAGAGGCACCUGAGUGAGCAAUCUGUCG&CGACAUUGCUCACAUUGCUUCCAGUAUUAC	((((...((((((.....(((((((((..((((&)))))))))))))..)))))).....))))	UGGAUGCAGCGAAAUUUACCUUCACCCCGCCGCAAGGCGUCACGGUAGAUGAUCAACGUAAGUAGAGGCACCUGAGUGAGCAAUCUGUCGCUCGAUUUUUCGGAUAAUACUUUUCAACCUCUGGCCGCGCGUAUGCGGCCAGAAAAUUUA	GCGAUCAGGAAGACCCUCGCGGAGAACCUGAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUAGCCAGCCGGGUGCUGGCUUUU	0.0239401	0.9496255	rarA	945505	recombination intermediate processing DNA-dependent ATPase

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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