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
STM1871	-72	-28	-46	-40	5.98	GcvB	143	187	154	160	6.86	-14.41	-27.25	-1.39714	UGGCGAUACAGGACAGGAAAUUACAACGGACGGUGGAUCAGGUAC&GUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCA	(((((.......(((...((((((.((((((((.((.....((((&)))).....)))))))))).....))))))..))).....)))))	GGCUGGCGAUACAGGACAGGAAAUUACAACGGACGGUGGAUCAGGUACAACUUCAUAGCGCAAAACCACACGCCAGUGGCGCUUAUUGAAAAACUAAAAGGAACGGACUCAUUCACUGUGUCCGCAUGGAUUGAUCGCUAUGAGGUUUUA	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0136032	0.7904009		1253392	putative phage integrase protein
STM3786	27	38	30	36	0.47	GcvB	178	189	180	186	2.94	-14.4	-17.81	-1.39617	UGUGGUGGUGUU&AGCACCGCCAUA	((((((((((((&))))))))))))	UCCUGACAGGCCAGAACGUCGACAGUUAUAAAUUUACCGUUAUGAUGGGCAUCCUGUUUGGUGACGGAUGUGCGCAUGAUUUGGUUGAUUCUGGCCACGUUUGUGGUGGUGUUUAUUGUGGGGUUUCGGGUGCUGACAUCGGAUACCCGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.013685	0.7904009	yicN	1255310	similar to E. coli orf hypothetical protein (AAC76686.1) Blastp hit to AAC76686.1 (159 aa) 82% identity in aa 10 - 159
STM2096	18	30	24	30	4.12	GcvB	152	164	152	158	1.44	-14.39	-19.95	-1.3952	UGGUAAGACAGGG&CCCUGUCUGUCCA	(((..((((((((&))))))))..)))	UACUCAAUGGGUAAACAAUGUUAAAAGUGGGGCGUAUCAGAGUUGGAUAGAACAGAACUAUGAAGGACGCCAGUAAUGAAUAUCUUACUUUUUGGUAAGACAGGGCAAGUAGGCUGGGAGUUGCAACGUUCUCUGGCACCGGUAGGGAAU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0137672	0.7904009	rfbD	1253617	dTDP-4-dehydrorhamnose reductase
STM0900	-48	-8	-15	-9	13.44	GcvB	36	81	37	43	10.87	-14.38	-38.69	-1.39423	ACAAUGCUGACCAUCACGCCAAAUUUUGCCCAGGAACGCGC&GCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGU	(((((((....((((((((((((....(((((.((((((((&))))))))...))))).))))))........))))))..)))))))	UCAUUAUCGCAUCGAUAUGGGGGCUGGACAAUGCUGACCAUCACGCCAAAUUUUGCCCAGGAACGCGCGCUGAACAUGCUGCGCCGCGACUGGAAGUCGCAUAAUACUUUUAUGGUGUAUGCACCCACUGGCAGCGGCAAAACGGGGUUA	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0138499	0.7904009		1252419	putative Fels-1 prophage DNA or RNA helicases of superfamily II
STM3564	-44	-17	-25	-19	1.58	GcvB	65	90	67	73	6.67	-14.37	-22.62	-1.39326	GCAAAAAACAAAACAUAUAACAUCACGA&UUGUGAUGUUGUGUUGUUGUGUUUGC	((((...(((.(((((((((((((((((&)))))))))))))).))).)))))))	UUUAUAAAAAGUACAGUCUGCUUUUUAACCAGCAAAAAACAAAACAUAUAACAUCACGAAUGGGGAUACAGGCACAUGAAACGGAAAGCGAAAACAAUAAUCGCAGGGAUUGUUGCAUUAGCAGUCUCGCAGGGGGCAAUGGCAGAUGAU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.013933	0.7904009	livK	1255087	leucine ABC transporter subunit substrate-binding protein LivK
STM2526	-32	-17	-31	-25	0.58	GcvB	71	86	79	85	3.06	-14.36	-18	-1.39229	ACAUAACAACAGAACA&UGUUGUGUUGUUGUGU	(((((((((((.((((&)))).)))))))))))	AUCCAUAGGCAAUUGAUGGGAUGCUCUUUAUAAUCCGCGCCUGACAUAACAACAGAACAUAUUUCAGAGGUAAACAUGGCUAUUGAACGGACUUUUUCCAUCAUUAAACCCAACGCGGUGGCAAAAAACGUUAUUGGCAGCAUCUUUGCG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0140165	0.7904009	ndk	1254048	nucleoside-diphosphate kinase
STM0022	-74	-55	-63	-57	2.39	GcvB	127	147	129	135	5.89	-14.36	-22.64	-1.39229	UGUUGGGAGGCGAGAAAGGG&CCCUUUUUCACUUCCUGUACA	(((..(((((.(((((((((&))))))))).)))))...)))	CUGUUGGGAGGCGAGAAAGGGGCGUUACGCGCGUCACUGCGCGUAACAAACCGACGGCAUCAGGAUAUUACGCAGAUGAAAAAAAACGUACCGAUUUUCCUUCGAUUAUUGCUACUGCUGUCGGCGGCCGGCCUGUCGUUUGCCGCGCAG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0140165	0.7904009	bcfB	1251540	fimbrial chaperone protein
STM1822	43	69	62	68	6.4	GcvB	162	185	163	169	6.16	-14.36	-26.92	-1.39229	GUGGUGAUCUACAAUAAUACGCUGUGG&CCAUAGUGAUUAAUGUAGCACCGC	((((((..(((((.((((.((((((((&)))))))))))).)))))))))))	GUUACAGAGGUGACGGCGGCGCCACAUUGUGGCAGUCUUGAACCAUUCAAAUGAAAAGCAAAUGAGGAAUAAGUAAUGUCUAUCGUGCGUAUUGAUGCCGAAGAUCGUUGGUCAGACGUGGUGAUCUACAAUAAUACGCUGUGGUAUACC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0140165	0.7904009	yoaB	1253341	similar to E. coli orf hypothetical protein (AAC74879.1) Blastp hit to AAC74879.1 (130 aa) 92% identity in aa 17 - 130
STM3076	-22	13	-22	-16	5.91	GcvB	35	75	69	75	10.97	-14.34	-31.22	-1.39035	CAACAUCCGAUCUGGAGUCAAAAUGUCCUCACGUA&UGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUG	((((((((((((...((((((((.((((.((((((&)))))).......))))))))))))...))))).)))))))	UUCCGGCGUAGCCCAAAACGCGCUGUCGUCAAGUCGUUACGGGCAUGGCCUUUCAACAUCCGAUCUGGAGUCAAAAUGUCCUCACGUAAAGAGCUUGCCAAUGCUAUUCGUGCGCUGAGCAUGGACGCAGUACAGAAAGCCAAGUCCGGU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0141849	0.7904009	tktA	1254599	transketolase
STM0470	27	75	69	75	7.67	GcvB	38	91	38	44	13.89	-14.3	-35.86	-1.38647	UGCAAAACAACGGCAUCCGGAUUGCCAGAUAGUCAAACGCAAAGGACGC&GUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCA	(((((((((((((((.(((....((((((.((((........(((((((&)))))))....))))))))))...)))...........))))))))).))))))	UGAUAGCGAAAGUAGCGCCGCACGCUUCCAGAAACGUUUCGGUCAUUUUAUCGGCGCUAAACGGGGGUAAAUGAAAUGCAGGUGUUAAACUCACUUCGCAAUGCAAAACAACGGCAUCCGGAUUGCCAGAUAGUCAAACGCAAAGGACGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0145273	0.7904009	rpmJ2	1251990	50S ribosomal protein L36

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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