Input and runtime details for job 6244847 (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 6244847 (server version trunk)

	Job Submitted & Queued		@ Fri Jan 07 21:36:19 CET 2022
	Pre-Processing Started		@ Fri Jan 07 21:36:23 CET 2022
	IntaRNA Started		@ Fri Jan 07 21:38:06 CET 2022
	IntaRNA Finished & Post-Processing		@ Fri Jan 07 21:38:48 CET 2022
	Post-Processing Finished		@ Fri Jan 07 21:39:11 CET 2022
	Job Completed		@ Fri Jan 07 21:39:12 CET 2022

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6244847&toolName=IntaRNA ( 30 days expiry )

Description of the job

ChiX - 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
b3657	20	30	22	28	1.81	ChiX	47	57	49	55	2.73	-11.21	-15.75	-1.18732	CCGUUAAAGAG&CUCUUUGACGG	(((((((((((&)))))))))))	AUAUUCGCUCUCACAGGGAUGGUUUACAAAAUGCGUUAUCGGUCUCAGCACCCCUAUAGCAUCAAGGAAAAGCAGAUGAAGAGUGAAGUGUUGUCCGUUAAAGAGAAAAUUGGUUAUGGCAUGGGAGACGCCGCCAGCCACAUUAUUUUC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0098469	0.8602904	yicJ	948168	putative xyloside transporter YicJ
b0228	26	36	27	33	4.14	ChiX	44	54	47	53	0.93	-8.24	-13.31	-0.872747	UCAAGGGGGGA&UUCCUCUUUGA	(((((((((((&)))))))))))	GCCGCUUUCCCGAUAUAAAACAACCUCAUUGCCAACCUUUCCUUUUCUUCUUACCGUUGAGAAAAAGGAGUCGCCAUGUCUGAAUAUCGUCGUUAUUACAUCAAGGGGGGAACAUGGUUUUUCACGGUGAAUUUACGAAAUCGUCGAAGC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.041862	0.8602904	rayT	944913	REP-associated tyrosine transposase
b1114	10	40	31	37	17.05	ChiX	46	73	49	55	11.33	-8.98	-37.36	-0.951125	CAAUAUCGUUAUACGCUGCCCGUCAAAGCGG&CCUCUUUGACGGGCCAAUAGCGAUAUUG	((((((((((((.....(((((((((((.((&)).)))))))))))..))))))))))))	UAAUGAACAGCAUUGCUUAUCAGAGAUAUGCCCCCAUAUGUUGAGGCAUAUCCUAACGAGAAUCUGACAACCGUUAUGCCUGAACAAUAUCGUUAUACGCUGCCCGUCAAAGCGGGUGAGCAGCGUCUGCUGGGCGAGUUAACCGGCGCA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0290804	0.8602904	mfd	945681	transcription-repair coupling factor
b1957	31	40	34	40	4.82	ChiX	46	55	46	52	0.92	-8.08	-13.82	-0.855801	GUUAAAGAGG&CCUCUUUGAC	((((((((((&))))))))))	UCGCACUGGCUAUUAUGCAAAAUUCGCCAUCUUCAACUAAGGUGAACAAGUUUCACUCGAAAAAAGGAGGCGAGUAUGAGCUUUAUGGUUAGUGAGGAAGUUACGGUUAAAGAGGGCGGCCCGCGGAUGAUUGUCACUGGAUACUCCAGC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0453019	0.8602904	yodC	946466	protein YodC
b0526	34	45	35	41	4.07	ChiX	41	52	45	51	0.86	-9.83	-14.76	-1.04115	AAAGAGGAAUUU&AAAUUCCUCUUU	((((((((((((&))))))))))))	GUAUGCUGAUUCGCGCGGGAAAUAUGGGUAUUAUACGCAACUCAAUUACCCACACAUGUCUAAACGGAAUCUUCGAUGCUAAAAAUCUUCAAUACUCUGACACGCCAAAAAGAGGAAUUUAAGCCUAUUCACGCCGGGGAAGUCGGCAUG	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0191875	0.8602904	cysS	946969	cysteine--tRNA ligase
b2835	36	46	40	46	3.27	ChiX	45	55	45	51	0.93	-11.4	-15.6	-1.20744	GUCGAAGGGGA&UCCUCUUUGAC	(((((((((((&)))))))))))	AGAUGCCAUUACUUGGCAGCGGCAAACCUGACUUUGUCACGUUGAAAAGCUGGGUAGACGAAGCGGAACAACACGAUGAGUGAGUCAGUGCACACUAACACUUCGUUGUGGUCGAAGGGGAUGAAAGCGGUUAUCGUGGCGCAGUUUCUC	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0089906	0.8602904	lplT	947317	lysophospholipid transporter
b1444	42	51	44	50	2.88	ChiX	44	53	45	51	0.92	-9.1	-12.9	-0.963835	CGAAGGGGAA&UUCCUCUUUG	((((((((((&))))))))))	UUGCCGAUCCUGGGGGCCUGGUGGCUAACCCGCGAAGGCGACAAUGGUCAAUAACCACUGAUACAGGAAUAUGCUAUGCAACAUAAGUUACUGAUUAACGGAGAACUGGUUAGCGGCGAAGGGGAAAAACAGCCUGUCUAUAAUCCGGCA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0274172	0.8602904	patD	945876	gamma-aminobutyraldehyde dehydrogenase
b3141	41	51	41	47	3.69	ChiX	38	48	42	48	1.04	-8.7	-13.43	-0.921468	AGGAAUUUCAU&AUGAAAUUCCU	(((((((((((&)))))))))))	AAAGCGCAUCCGGUGCUGUUAAUCGGCGUGACUUUUGUGCUCUCUAUUGUUUGUUCCGCAUUCGGCAUUUUGUAAAUGGAACGAGGCACUGCGUCUGGUGGUGCCUCUUUACUUAAGGAAUUUCAUCCUGUGCAAACCCUUCAGCAAGUU	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0333715	0.8602904	agaI	947985	putative deaminase AgaI
b0847	24	53	46	52	5.92	ChiX	26	55	27	33	1.18	-10.7	-17.8	-1.1333	GUUAAAUGGGAAUUACAUUCUGUUAUUAUU&AAUAAUAAAAAAAUGAAAUUCCUCUUUGAC	((((((..((((((.((((...((((((((&))))))))...)))).))))))..))))))	GAAUUCUGGUAAAAAACAUUAUCGUAAAUUACCAUUUCUUUCAACAGCUUACUAGUAAACAAGAAGUUAGCCUCCGUGAAUAUAAACGUCGCCGAAUUGUUAAAUGGGAAUUACAUUCUGUUAUUAUUUGUGGUCCUCGCGCUUGGGCUA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0125842	0.8602904	ybjL	945474	putative transport protein YbjL
b2768	44	53	46	52	1.52	ChiX	48	57	49	55	2.73	-8.45	-12.7	-0.894989	CCGUUAAAGA&UCUUUGACGG	((((((((((&))))))))))	CACUACAACAGUGGCGCUAUCCGCCUUCCGGAUUCGGCAUCACCUACCGCUUUGGAUAAAUAAUAAGGAUAAUUUAUGCCCCUCUUACACCUGCUCCGCCAGAAUCCGGUGAUUGCUGCCGUUAAAGAUAAUGCCAGCCUGCAACUGGCA	ACACCGUCGCUUAAAGUGACGGCAUAAUAAUAAAAAAAUGAAAUUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU	0.0377438	0.8602904	ygcP	947536	putative anti-terminator regulatory 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 3.2.0 linking Vienna RNA package 2.4.14

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