Input and runtime details for job 4935127 (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_003197
	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 4935127 (server version trunk)

	Job Submitted & Queued		@ Mon Jan 27 14:12:23 CET 2020
	IntaRNA Started		@ Mon Jan 27 14:14:40 CET 2020
	IntaRNA Finished & Post-Processing		@ Mon Jan 27 14:16:11 CET 2020
	Post-Processing Finished		@ Mon Jan 27 14:17:25 CET 2020
	Job Completed		@ Mon Jan 27 14:17:35 CET 2020

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4935127&toolName=IntaRNA ( 30 days expiry )

Description of the job

GcvB - 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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
STM1564	19	40	32	38	3.82	GcvB	72	90	74	80	4.11	-16.06	-23.99	-1.55712	GCAAAUACCUCAGCAGCACAAC&GUUGUGUUGUUGUGUUUGC	((((((((...(((((((((((&)))))))))))))))))))	AAUAUUUGCCAUGCUGAAUACGAAUUAAUUUUCUGCGAGCCGUACUAAAUAAAUACAUGUUCACGGAGGCAUUAUAUGUUUACUUAUCACUCAGCAAAUACCUCAGCAGCACAACCGGCCCUGGUCAACGCGAUUGAACAAGGAUUACGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.004788	0.6975035	yddX	1253082	biofilm-dependent modulation protein
STM3609	2	53	15	21	10.96	GcvB	25	91	71	77	19.1	-17.04	-47.1	-1.65213	UGCAAGCAACCGCCACAACACUCGACCAUGAGCAGGAACAUGUUCCGGUAAA&UUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCA	((((((((.....(((((((..(((((.(((((..(((((((((((((((((&))))))))))..))))))).............))))).)))))...)))))))......))))))))	CUUUUGUUACACAUUGAAAUAUAACUUUUGCUGUGCGUAAUAUGGCUAUUCGUUCGCUAAAAAUAAGAAAAUAGUAUGCAAGCAACCGCCACAACACUCGACCAUGAGCAGGAACAUGUUCCGGUAAACUCACGCAAUAAAGUCGUUAUU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0024321	0.659913	yhjE	1255132	MFS transporter
STM2745	-21	11	-6	1	8.34	GcvB	36	61	44	50	5.69	-14.8	-28.83	-1.43495	UGAGCCGACUGAUACCCCAUCAUGAAACGCGC&GCGUGUUCUGAUGGGCUUUUGGCUUA	((((((((.......(((((((.((.((((((&)))))))))))))))...))))))))	AAUCCGUCAGUGGCAACAGCGCCGCACCGUCAUCCGUUAAUCCACGCUCAGGGAUGAGCCGACUGAUACCCCAUCAUGAAACGCGCGCCCUUUCUCUGUAAGCAGUCUCCGGACCGCACGCUCGAAGUGGUGAUCCUUGCCGGAAGCCUG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0107353	0.7904009		1254268
STM1879	-34	15	6	12	6.01	GcvB	49	86	52	58	10.91	-14.44	-31.36	-1.40005	AUAUAACAAAUAUUAACGCAAAAGAAAAAACGACAUGUUGCCAAAAGCC&GGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGU	((((((((.......((((((........(((((..((.((((((((((&))))))))))..)).)))))....))))))))))))))	ACCGGGACUACCAUGCUACGCCGCUGUGUUUGCCGCGUGAUAUAUAACAAAUAUUAACGCAAAAGAAAAAACGACAUGUUGCCAAAAGCCAAUCGAAUUCCCUAUGCCAUGACCGUACAUGGCGAUACGCGCAUUGAUAAUUAUUACUGG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0133605	0.7904009	ptrB	1253400	oligopeptidase B
STM3089	56	73	67	73	1.87	GcvB	157	174	157	163	3.11	-16.07	-21.05	-1.55809	UUAAUCAGUAUGGAUGGA&UCUGUCCAUAGUGAUUAA	(((((((.((((((((((&)))))))))).)))))))	GUAAAAAGGUGUUUUGCCAUAUUUAAUUUCACCUAAGGAGAAUUUAGUUAGCUCAAACUGUUGUGCGGAAUAGUCAUGACAGAAGAUUCUACCAUGAGUCUGAAGGUUGCUGACACUGGCAGUCUGAGUGUUAAUCAGUAUGGAUGGAUU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0047561	0.6975035	yqgD	1254612	similar to E. coli orf hypothetical protein (AAC75978.1) Blastp hit to AAC75978.1 (83 aa) 52% identity in aa 1 - 78
STM4250	10	38	18	24	10.09	GcvB	49	80	66	72	9.49	-14.64	-34.22	-1.41944	CAGCGCACCAUUACACUGAGCGAGAAGCC&GGCUUUUGGCUUACGGUUGUGAUGUUGUGUUG	(((((((.(((((((((((((.(((((((&))))))).)))..))).))))))).)))))))	CCCCGCUGGCUUUUACCUUUUCCAGACUUGCUGCACACUAUUCAGGAGACGUUUGUUUUUAGGAAGGAGCAGCCUAUGUGGUAUCAGCGCACCAUUACACUGAGCGAGAAGCCGCGCGGGUUUCAUCUGAUAACAGAUGAAAUUACCGAU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0118389	0.7904009	yjbQ	1255776	similar to E. coli orf hypothetical protein (AAC77026.1) Blastp hit to AAC77026.1 (138 aa) 78% identity in aa 1 - 138
STM3344	-70	-27	-61	-55	11.46	GcvB	48	102	83	89	15.57	-18.35	-45.38	-1.77915	CGCGGGCAACGAGCACAACCACGCGGCACAGCAACCGCAAGUUC&GGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCG	(((((((..((((((((((.((((((((((.((((((.((((((&))))))........)))))))).)))))))).))))))))))......)))))))	GUUUACGCGGGCAACGAGCACAACCACGCGGCACAGCAACCGCAAGUUCUUGACAUCUAAUCGGGAUUAUAGGCAAUGGCUGAAAAUCAAUACUACGGCACUGGUCGCCGCAAAAGUUCCGCAGCUCGCGUGUUCAUCAAACCGGGCAAC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0009093	0.4343002	rpsI	1254867	30S ribosomal protein S9
STM0412	27	72	27	33	5.33	GcvB	35	73	67	73	10.95	-14.92	-31.2	-1.44659	ACAUUACUUCCGGCGAUGCCACCAGCCUAAAAACAGACCUGUCGCA&UGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGU	(((((((..((......((((..((((((....((((.....((((&))))...)))).))))))..))))....))..)))))))	GUCGUGGGUUACAACUUCUAAACCUGCAAAAAAGGCCAGAGGUCGUCCUCUGGCCCGUUUCGGGCGCAUGCUGCCAUGCGGCGGCGAGUCGCGCCCACUUCACAUUACUUCCGGCGAUGCCACCAGCCUAAAAACAGACCUGUCGCAAUC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.009969	0.7883581		2673775	putative inner membrane protein
STM0001	-71	-15	-35	-29	4	GcvB	141	186	155	161	8.64	-18.71	-31.35	-1.81405	GGCGGGCAGAUACUUUAACCAAUAUAGGAAUACAAGACAGACAAAUAAAAAUGACAG&CUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCC	(((((((...(((.((((.((.(((.((........(((((((......((((((((&)))).)))).....)))))))))))).)).)))).))))).)))))	CUUAGGCGGGCAGAUACUUUAACCAAUAUAGGAAUACAAGACAGACAAAUAAAAAUGACAGAGUACACAACAUCCAUGAACCGCAUCAGCACCACCACCAUUACCACCAUCACCAUUACCACAGGUAACGGUGCGGGCUGACGCGUACAG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0006816	0.3847632	thrL	1251519	thr operon leader peptide
STM3630	-43	-2	-21	-15	6.19	GcvB	51	92	66	72	10.1	-20.93	-37.22	-2.02929	UUGCAAAGGGCAAAACAACAUACAUCACAAUUGGAGCAGAAG&CUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAA	(((((((...((.((((((((((((((((((((.((((((((&)))))).))..))))))))))).))))))))).)))))))))	AAAAAACAAAAAAGGCCGGGCGGUAAAAGCCUUUGCAAAGGGCAAAACAACAUACAUCACAAUUGGAGCAGAAGAAUGAGUAUUUCCUUGAAGAAGUCAGGGAUGCUGAAGCUUGGUUUGAGCCUGGUGGCCAUGACCGUUGCAGCAAGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	9.35e-05	0.2036716	dppA	1255154	ABC transporter substrate-binding 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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