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
STM3236	25	40	34	40	5.36	GcvB	154	169	154	160	2.34	-15.54	-23.24	-1.5067	CAAUGUGGACAGGCAG&CUGUCUGUCCAUAGUG	((.(((((((((((((&))))))))))))).))	CCGGGCAGAAUAUCUGGCUAACAAUGCAGCGUCCAGCCCCUUAACAUAAAAGGAAGUAAAGAGAGGUUAAUAACGAUGAUUACGACCCGAACCGCCAAACAAUGUGGACAGGCAGACUACGGAUGGCUACAGGCCCGCUAUACCUUCUCC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0067362	0.7419678	yhaK	1254759	similar to E. coli orf hypothetical protein (AAC76141.1) Blastp hit to AAC76141.1 (233 aa) 84% identity in aa 1 - 233
STM3574	-53	-35	-43	-37	7.7	GcvB	150	169	152	158	2.39	-15.48	-25.57	-1.50088	CACUAUAACGGGCAGGGUA&UACCCUGUCUGUCCAUAGUG	((((((.((((((((((((&))))))))))))..))))))	GGCCGUGACGGUCAGAUGACAACACUAUAACGGGCAGGGUAUGCUUAUUUCCGCAUUUUCUGACAGGUUAACAGUAUGAGUAAGCCACCGCUUUUCUUCAUUAUAAUCAUUGCAUUAAUCGUAGUUGCCGCGUCGUUCCGCUUCGUUCAG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0070016	0.7528387	yhhM	1255097	similar to E. coli putative receptor (AAC76492.1) Blastp hit to AAC76492.1 (119 aa) 84% identity in aa 1 - 116
STM1749	51	71	52	58	3.05	GcvB	36	55	48	54	5.61	-15.39	-24.05	-1.49216	AAAAGCCCAGCGUGAAUAUGC&GCGUGUUCUGAUGGGCUUUU	(((((((((....((((((((&))))))))...)))))))))	UAUCGUCGAUCUGUCUAUACUCACGUAUCGCGCAGAUGAUUUACUAAAAAAGUUUAACAUUAUCAGGAGAGCAUUAUGGCUGUUACUAAUGUCGCUGAACUUAACGCACUCGUAGAGCGUGUAAAAAAAGCCCAGCGUGAAUAUGCCAGU	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0074172	0.7711365	adhE	1253268	bifunctional acetaldehyde-CoA/alcohol dehydrogenase
STM3567	-51	-28	-45	-39	4.12	GcvB	63	87	75	81	7.58	-15.35	-27.05	-1.48828	AACACCACAACACACGUAACAACC&GGUUGUGAUGUUGUGUUGUUGUGUU	(((((.(((((((((((.((((((&)))))).)))).))))))).)))))	AAUCGAAAUAAAGUGCUGAACAAUAACACCACAACACACGUAACAACCAGAAUAAUGGGGAUUAUCAGGAUGAAUAUGAAGGGUAAAACGUUAUUGGCAGGAUGUAUCGCCCUGUCAUUAAGCCAUAUGGCAUUCGCCGACGACAUUAAA	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0076089	0.7711365	livJ	1255090	high-affinity branched-chain amino acid transporter
STM2189	-6	10	2	8	3.03	GcvB	155	171	158	164	2.56	-15.31	-20.9	-1.4844	AUCAUUAUGGGCAGCA&UGUCUGUCCAUAGUGAU	((((((((((((((((&)).))))))))))))))	CGCAGACCGGAUAACGUAUUUCUUUUGCCAUCCGGCGCGGAUAGUCAUAAUUAAAAAGGCCGACAGGGUAUCAUUAUGGGCAGCACGAUUUCUCCGCCGUCGGGUGAAUAUUUGUUGGAAAUGCGUGGCAUUAACAAAUCAUUUCCCGGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0078051	0.7711365	mglA	1253711	galactose/methyl galactoside ABC transporter ATP-binding protein MglA
STM1129	-11	38	28	34	12.17	GcvB	139	186	143	149	8.7	-15.3	-36.17	-1.48343	GGCGGAACUGGAUGUCACUAUUAGCCAGGCUGGAACAAAGUGUACACGA&UCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCC	(((((..((..((.(((((((....(((((.((....(((((((((.((&)).)))))))))..)).)))))...)))))))...))..))..)))))	UUUUGCUUGAUGUAGCAACACUCCAAGACAUAACAUAAAACGGAGCAAAACUUCAAAUAUAUAAGGCGGAACUGGAUGUCACUAUUAGCCAGGCUGGAACAAAGUGUACACGAAAACGGUGGGCUGAUUGUCUCAUGCCAACCGGUACCA	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0078548	0.7711365		1252647	N-acetylmannosamine-6-phosphate 2-epimerase
STM1571	-69	-46	-53	-47	3	GcvB	65	89	66	72	6.66	-15.24	-24.9	-1.47761	CAGUCACAAAGCAUGACAUCACAA&UUGUGAUGUUGUGUUGUUGUGUUUG	((..((((((((((((((((((((&))))))))))))))).)))))..))	UCAGGACAGUCACAAAGCAUGACAUCACAAAAAGCAACGCUAAUAGGGCUUGUUGCCAUCGUUCUGUGGAGCACGAUGGUUGGGUUAAUUCGCGGCGUCAGCGAAGGUCUCGGACCGGUAGGCGGCGCAGCCAUGAUCUAUUCAUUAAGC	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0081593	0.7799855	yddG	1253089	putative permease
STM2801	35	49	42	48	3.54	GcvB	151	164	152	158	1.44	-15.18	-20.16	-1.47179	UGGAAAAGGCAGGGU&ACCCUGUCUGUCCA	((((..(((((((((&))))))))).))))	UGGACUUUUCUGAAAGCGUUGAUAACGCGCUAUCGGGUAAGGUAAGCCCGCAGUACAAGAGAAUGAGGAUAAAAUAUGUAUUUACGACCUGACGAGGUGGCGCGGGUACUGGAAAAGGCAGGGUUUACCGUCGAUGUGGUGACGAAUAAG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0084743	0.7799855	ygaC	1254324	similar to E. coli orf hypothetical protein (AAC75718.1) Blastp hit to AAC75718.1 (114 aa) 88% identity in aa 1 - 112
STM3523	7	24	10	16	5.8	GcvB	72	89	80	86	4.11	-15.15	-25.06	-1.46889	CAAACACAACGGCAUGAC&GUUGUGUUGUUGUGUUUG	((((((((((((((((((&))))))))))))))))))	UCGAGAUAUUUUUCCAGGCCGGGUAGGGCGAAUGCCGCUAUCCGGCGCAAGGUUGGUUACUUUCAGAGAUUAUUCAUGAAACAAACACAACGGCAUGACGCGAUCAUUGAACUGGUAAAAAAACAGGGGUACGUCAGUACGGAAGAGCUG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0086358	0.7799855	glpR	1255046	DeoR/GlpR family transcriptional regulator
STM3598	58	75	64	70	4.01	GcvB	62	79	67	73	5.83	-15.15	-24.99	-1.46889	AGCACAACGUCACUACCG&CGGUUGUGAUGUUGUGUU	(((((((((((((.((((&)))).)))))))))))))	AAAUGGUUCUGGCCUGAUUGUUAUUCAUGUUUUUAUAGCACACGCCACUUAUUAUUUUUAAUUCAGAGGAAGAAAAUGAAAAUUAGAGUUUUCAUGGCCACCGUGUUGCUGCUCAUCAGCCACUGUGUAUUUAGCACAACGUCACUACCG	ACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGCUUU	0.0086358	0.7799855		1255121	putative L-asparaginase

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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