Input and runtime details for job 1765463 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation
46	0.009202	0.6129	b0183	rnhB	-8.44	0.085048	25 -- 32	48 -- 55	ribonuclease HII degrades RNA of DNA-RNA hybrids	_____________24_______33\n_____________\|________\|\n5'-AAU...AGUUA________AUUAU...UCC-3'\n______________GUCAAAGA\n______________\|\|\|\|\|\|\|\|\n______________CAGUUUCU\n3'-UUU...CCGGG________CCUUA...ACA-5'\n_____________\|________\|\n_____________56_______47\n	26 -- 32	48 -- 54	-9.30452 kcal/mol	0.544993 kcal/mol	0.318869 kcal/mol	24 33@LB@ \| \|@LB@5'-AAU...AGUUA AUUAU...UCC-3'@LB@ GUCAAAGA@LB@ \|\|\|\|\|\|\|\|@LB@ CAGUUUCU@LB@3'-UUU...CCGGG CCUUA...ACA-5'@LB@ \| \|@LB@ 56 47@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -9.30452 kcal/mol@LB@Unfolding Energy - mRNA 0.544993 kcal/mol@LB@Unfolding Energy - sRNA 0.318869 kcal/mol@LB@@LB@Position - mRNA 25 -- 32@LB@Position - sRNA 48 -- 55@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 48 -- 54@LB@
107	0.02168	0.6177	b1738	chbB	-9.32	0.056668	26 -- 34	47 -- 55	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________25________35\n_____________\|_________\|\n5'-AAU...CACAG_________AAACA...CGG-3'\n______________GUCAAGGAG\n______________\|\|\|\|\|:\|\|\|\n______________CAGUUUCUC\n3'-UUU...CCGGG_________CUUAA...ACA-5'\n_____________\|_________\|\n_____________56________46\n	28 -- 34	47 -- 53	-13.6925 kcal/mol	3.47679 kcal/mol	0.899516 kcal/mol	25 35@LB@ \| \|@LB@5'-AAU...CACAG AAACA...CGG-3'@LB@ GUCAAGGAG@LB@ \|\|\|\|\|:\|\|\|@LB@ CAGUUUCUC@LB@3'-UUU...CCGGG CUUAA...ACA-5'@LB@ \| \|@LB@ 56 46@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -13.6925 kcal/mol@LB@Unfolding Energy - mRNA 3.47679 kcal/mol@LB@Unfolding Energy - sRNA 0.899516 kcal/mol@LB@@LB@Position - mRNA 26 -- 34@LB@Position - sRNA 47 -- 55@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 47 -- 53@LB@
136	0.02642	0.6177	b4036	lamB	-8.19	0.095416	26 -- 54	55 -- 84	maltose outer membrane porin (maltoporin)	_____________25_____________________________55\n_____________\|______________________________\|\n5'-CGC...GGUAG_____________CAU_______C______CCGCC...GUU-3'\n______________AAGAAGGU_GCCA___UCGCUAU_GGCCUG\n______________\|\|:\|\|::\|_\|\|\|\|___\|\|\|\|\|\|\|_\|\|\|\|:\|\n______________UUUUUUUA_CGGU___AGCGAUA_CCGGGC\n___________3'-________C____UAU_______A______AGUUU...ACA-5'\n______________\|_____________________________\|\n______________84____________________________54\n	41 -- 47	62 -- 68	-32.2235 kcal/mol	10.7352 kcal/mol	13.2983 kcal/mol	25 55@LB@ \| \|@LB@5'-CGC...GGUAG CAU C CCGCC...GUU-3'@LB@ AAGAAGGU GCCA UCGCUAU GGCCUG@LB@ \|\|:\|\|::\| \|\|\|\| \|\|\|\|\|\|\| \|\|\|\|:\|@LB@ UUUUUUUA CGGU AGCGAUA CCGGGC@LB@ 3'- C UAU A AGUUU...ACA-5'@LB@ \| \|@LB@ 84 54@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -32.2235 kcal/mol@LB@Unfolding Energy - mRNA 10.7352 kcal/mol@LB@Unfolding Energy - sRNA 13.2983 kcal/mol@LB@@LB@Position - mRNA 26 -- 54@LB@Position - sRNA 55 -- 84@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 62 -- 68@LB@
156	0.03128	0.6177	b4512	ybdD	-7.87	0.110479	26 -- 38	43 -- 55	DUF466 family protein	_____________25____________39\n_____________\|_____________\|\n5'-GCA...UCAGA__G__________GUUGG...GGG-3'\n______________GU_AGGGGGGGAU\n______________\|\|_\|::\|:\|\|:\|\|\n______________CA_UUUCUCCUUA\n3'-UUU...CCGGG__G__________AAGUA...ACA-5'\n_____________\|_____________\|\n_____________56____________42\n	32 -- 38	43 -- 49	-14.3671 kcal/mol	5.55181 kcal/mol	0.946481 kcal/mol	25 39@LB@ \| \|@LB@5'-GCA...UCAGA G GUUGG...GGG-3'@LB@ GU AGGGGGGGAU@LB@ \|\| \|::\|:\|\|:\|\|@LB@ CA UUUCUCCUUA@LB@3'-UUU...CCGGG G AAGUA...ACA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -7.87 kcal/mol@LB@Hybridization Energy -14.3671 kcal/mol@LB@Unfolding Energy - mRNA 5.55181 kcal/mol@LB@Unfolding Energy - sRNA 0.946481 kcal/mol@LB@@LB@Position - mRNA 26 -- 38@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 43 -- 49@LB@
37	0.007616	0.6129	b4141	yjeH	-11.12	0.024259	30 -- 40	44 -- 54	putative transporter	_____________29__________41\n_____________\|___________\|\n5'-CAG...CCCCU___________AAAGA...CUG-3'\n______________UCAAGGGGGAA\n______________\|\|\|\|:\|:\|\|\|\|\n______________AGUUUCUCCUU\n3'-UUU...CGGGC___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	34 -- 40	44 -- 50	-14.4219 kcal/mol	2.36204 kcal/mol	0.939671 kcal/mol	29 41@LB@ \| \|@LB@5'-CAG...CCCCU AAAGA...CUG-3'@LB@ UCAAGGGGGAA@LB@ \|\|\|\|:\|:\|\|\|\|@LB@ AGUUUCUCCUU@LB@3'-UUU...CGGGC AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.4219 kcal/mol@LB@Unfolding Energy - mRNA 2.36204 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 30 -- 40@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 44 -- 50@LB@
32	0.006131	0.6129	b2585	pssA	-9.74	0.046374	32 -- 41	45 -- 54	phosphatidylserine synthase; CDP-diacylglycerol-serine O-phosphatidyltransferase	_____________31_________42\n_____________\|__________\|\n5'-CGC...CCAGC__________GAUCG...CCG-3'\n______________UCGAAGAGGG\n______________\|\|:\|\|\|\|\|\|:\n______________AGUUUCUCCU\n3'-UUU...CGGGC__________UAAAG...ACA-5'\n_____________\|__________\|\n_____________55_________44\n	35 -- 41	45 -- 51	-13.2862 kcal/mol	2.61225 kcal/mol	0.929144 kcal/mol	31 42@LB@ \| \|@LB@5'-CGC...CCAGC GAUCG...CCG-3'@LB@ UCGAAGAGGG@LB@ \|\|:\|\|\|\|\|\|:@LB@ AGUUUCUCCU@LB@3'-UUU...CGGGC UAAAG...ACA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -13.2862 kcal/mol@LB@Unfolding Energy - mRNA 2.61225 kcal/mol@LB@Unfolding Energy - sRNA 0.929144 kcal/mol@LB@@LB@Position - mRNA 32 -- 41@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 45 -- 51@LB@
123	0.02427	0.6177	b4485	ytfR	-5.89	0.261942	32 -- 42	44 -- 54	putative sugar ABC transporter ATPase	_____________31__________43\n_____________\|___________\|\n5'-CCU...AAGAA_______A___GAAAA...GCC-3'\n______________UUAGAGA_GAA\n______________\|:\|:\|\|\|_\|\|\|\n______________AGUUUCU_CUU\n3'-UUU...CGGGC_______C___AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	32 -- 38	48 -- 54	-7.06152 kcal/mol	0.22708 kcal/mol	0.939671 kcal/mol	31 43@LB@ \| \|@LB@5'-CCU...AAGAA A GAAAA...GCC-3'@LB@ UUAGAGA GAA@LB@ \|:\|:\|\|\| \|\|\|@LB@ AGUUUCU CUU@LB@3'-UUU...CGGGC C AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -5.89 kcal/mol@LB@Hybridization Energy -7.06152 kcal/mol@LB@Unfolding Energy - mRNA 0.22708 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 32 -- 42@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 48 -- 54@LB@
146	0.02871	0.6177	b1120	cobB	-8.56	0.080407	32 -- 40	43 -- 51	deacetylase of acs and cheY chemotaxis regulator	_____________31________41\n_____________\|_________\|\n5'-CGC...GAUGC_________GCGUG...AUC-3'\n______________GGGAGGAAU\n______________::\|\|\|\|\|\|\|\n______________UUCUCCUUA\n3'-UUU...GCAGU_________AAGUA...ACA-5'\n_____________\|_________\|\n_____________52________42\n	34 -- 40	43 -- 49	-11.3695 kcal/mol	1.94725 kcal/mol	0.859837 kcal/mol	31 41@LB@ \| \|@LB@5'-CGC...GAUGC GCGUG...AUC-3'@LB@ GGGAGGAAU@LB@ ::\|\|\|\|\|\|\|@LB@ UUCUCCUUA@LB@3'-UUU...GCAGU AAGUA...ACA-5'@LB@ \| \|@LB@ 52 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -11.3695 kcal/mol@LB@Unfolding Energy - mRNA 1.94725 kcal/mol@LB@Unfolding Energy - sRNA 0.859837 kcal/mol@LB@@LB@Position - mRNA 32 -- 40@LB@Position - sRNA 43 -- 51@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 43 -- 49@LB@
183	0.03803	0.6177	b3616	tdh	-7.63	0.122830	33 -- 50	37 -- 52	L-threonine 3-dehydrogenase NAD(P)-binding	_____________32_________________51\n_____________\|__________________\|\n5'-UAG...UGCAA________C____A____ACCGG...GUA-3'\n______________AAAGAGGG_AUUU_CGUU\n______________\|\|\|\|\|\|\|:_\|\|\|\|_\|:\|\|\n______________UUUCUCCU_UAAA_GUAA\n3'-UUU...GGCAG__________________AAAAA...ACA-5'\n_____________\|__________________\|\n_____________53_________________36\n	34 -- 40	45 -- 51	-11.8553 kcal/mol	3.14412 kcal/mol	1.07641 kcal/mol	32 51@LB@ \| \|@LB@5'-UAG...UGCAA C A ACCGG...GUA-3'@LB@ AAAGAGGG AUUU CGUU@LB@ \|\|\|\|\|\|\|: \|\|\|\| \|:\|\|@LB@ UUUCUCCU UAAA GUAA@LB@3'-UUU...GGCAG AAAAA...ACA-5'@LB@ \| \|@LB@ 53 36@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -11.8553 kcal/mol@LB@Unfolding Energy - mRNA 3.14412 kcal/mol@LB@Unfolding Energy - sRNA 1.07641 kcal/mol@LB@@LB@Position - mRNA 33 -- 50@LB@Position - sRNA 37 -- 52@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 45 -- 51@LB@
161	0.03295	0.6177	b1630	rsxD	-5.86	0.265655	34 -- 42	49 -- 57	SoxR iron-sulfur cluster reduction factor component; putative membrane protein of electron transport complex	_____________33________43\n_____________\|_________\|\n5'-AGC...AGCUG_________CGGCU...CAG-3'\n______________CCGUCGAAG\n______________\|\|\|\|\|:\|\|\|\n______________GGCAGUUUC\n3'-UUU...AACCG_________UCCUU...ACA-5'\n_____________\|_________\|\n_____________58________48\n	36 -- 42	49 -- 55	-12.0908 kcal/mol	3.50131 kcal/mol	2.72876 kcal/mol	33 43@LB@ \| \|@LB@5'-AGC...AGCUG CGGCU...CAG-3'@LB@ CCGUCGAAG@LB@ \|\|\|\|\|:\|\|\|@LB@ GGCAGUUUC@LB@3'-UUU...AACCG UCCUU...ACA-5'@LB@ \| \|@LB@ 58 48@LB@@LB@@LB@Energy -5.86 kcal/mol@LB@Hybridization Energy -12.0908 kcal/mol@LB@Unfolding Energy - mRNA 3.50131 kcal/mol@LB@Unfolding Energy - sRNA 2.72876 kcal/mol@LB@@LB@Position - mRNA 34 -- 42@LB@Position - sRNA 49 -- 57@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 49 -- 55@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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When using CopraRNA please cite :

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.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
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 CopraRNA version 2.1.2

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