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
181	0.03769	0.6177	b0912	ihfB	-7.34	0.140491	192 -- 199	43 -- 50	integration host factor (IHF) DNA-binding protein beta subunit	_____________191______200\n_____________\|________\|\n5'-ACG...GAACC________CAUGA...UGG-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	193 -- 199	43 -- 49	-10.3812 kcal/mol	2.20002 kcal/mol	0.845564 kcal/mol	191 200@LB@ \| \|@LB@5'-ACG...GAACC CAUGA...UGG-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -7.34 kcal/mol@LB@Hybridization Energy -10.3812 kcal/mol@LB@Unfolding Energy - mRNA 2.20002 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 192 -- 199@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 43 -- 49@LB@
182	0.03771	0.6177	b0397	sbcC	-11.00	0.025718	84 -- 100	39 -- 56	exonuclease dsDNA ATP-dependent	_____________83_________________101\n_____________\|__________________\|\n5'-GAA...CUCAG___________UG_____AUCGC...UUG-3'\n______________CGUCGAAGAGG___UUCA\n______________\|\|\|\|:\|\|\|\|\|\|___\|\|\|\|\n______________GCAGUUUCUCC___AAGU\n3'-UUU...ACCGG___________UUA____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	88 -- 94	46 -- 52	-19.0672 kcal/mol	6.9127 kcal/mol	1.15786 kcal/mol	83 101@LB@ \| \|@LB@5'-GAA...CUCAG UG AUCGC...UUG-3'@LB@ CGUCGAAGAGG UUCA@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ GCAGUUUCUCC AAGU@LB@3'-UUU...ACCGG UUA AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -19.0672 kcal/mol@LB@Unfolding Energy - mRNA 6.9127 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 84 -- 100@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 46 -- 52@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@
184	0.03803	0.6177	b3647	ligB	-3.67	0.590336	72 -- 111	39 -- 67	DNA ligase NAD(+)-dependent	_____________71________________________________________112\n_____________\|_________________________________________\|\n5'-GGC...GCUUC_______U________UUCACUGCAAUA____C__U_____GGAAG...AAA-3'\n______________CGC_AUU_GCCUGUCA____________AAGA_GA_UUUCA\n______________\|\|\|_\|\|\|_\|\|\|:\|\|\|\|____________\|\|\|\|_\|\|_\|\|\|\|\|\n______________GCG_UAA_CGGGCAGU____________UUCU_CU_AAAGU\n3'-UUU...UUAUA___A___C________________________C__U_____AAAAA...ACA-5'\n_____________\|_________________________________________\|\n_____________68________________________________________38\n	80 -- 86	52 -- 58	-24.1741 kcal/mol	6.974 kcal/mol	13.5271 kcal/mol	71 112@LB@ \| \|@LB@5'-GGC...GCUUC U UUCACUGCAAUA C U GGAAG...AAA-3'@LB@ CGC AUU GCCUGUCA AAGA GA UUUCA@LB@ \|\|\| \|\|\| \|\|\|:\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|@LB@ GCG UAA CGGGCAGU UUCU CU AAAGU@LB@3'-UUU...UUAUA A C C U AAAAA...ACA-5'@LB@ \| \|@LB@ 68 38@LB@@LB@@LB@Energy -3.67 kcal/mol@LB@Hybridization Energy -24.1741 kcal/mol@LB@Unfolding Energy - mRNA 6.974 kcal/mol@LB@Unfolding Energy - sRNA 13.5271 kcal/mol@LB@@LB@Position - mRNA 72 -- 111@LB@Position - sRNA 39 -- 67@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 52 -- 58@LB@
185	0.03847	0.6177	b0621	dcuC	-6.69	0.186516	155 -- 171	26 -- 48	anaerobic C4-dicarboxylate transport	_____________154_____________________172\n_____________\|_______________________\|\n5'-UGC...GCUUU_______________________UACUU...UCG-3'\n______________AGGAAUUUU______UUAUUAUU\n______________\|\|\|\|\|\|\|\|:______\|\|\|\|\|\|\|\|\n______________UCCUUAAAG______AAUAAUAA\n3'-UUU...GUUUC_________UAAAAA________UACGG...ACA-5'\n_____________\|_______________________\|\n_____________49______________________25\n	165 -- 171	26 -- 32	-10.8714 kcal/mol	3.1068 kcal/mol	1.07117 kcal/mol	154 172@LB@ \| \|@LB@5'-UGC...GCUUU UACUU...UCG-3'@LB@ AGGAAUUUU UUAUUAUU@LB@ \|\|\|\|\|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UCCUUAAAG AAUAAUAA@LB@3'-UUU...GUUUC UAAAAA UACGG...ACA-5'@LB@ \| \|@LB@ 49 25@LB@@LB@@LB@Energy -6.69 kcal/mol@LB@Hybridization Energy -10.8714 kcal/mol@LB@Unfolding Energy - mRNA 3.1068 kcal/mol@LB@Unfolding Energy - sRNA 1.07117 kcal/mol@LB@@LB@Position - mRNA 155 -- 171@LB@Position - sRNA 26 -- 48@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 26 -- 32@LB@
186	0.03879	0.6177	b2898	ygfZ	-4.98	0.377094	224 -- 230	51 -- 57	iron-sulfur cluster repair protein plumbagin resistance	_____________223_____231\n_____________\|_______\|\n5'-CGU...CCUCC_______CCUAC...CUG-3'\n______________CCGUCAG\n______________\|\|\|\|\|\|:\n______________GGCAGUU\n3'-UUU...AACCG_______UCUCC...ACA-5'\n_____________\|_______\|\n_____________58______50\n	224 -- 230	51 -- 57	-9.02345 kcal/mol	1.32881 kcal/mol	2.71582 kcal/mol	223 231@LB@ \| \|@LB@5'-CGU...CCUCC CCUAC...CUG-3'@LB@ CCGUCAG@LB@ \|\|\|\|\|\|:@LB@ GGCAGUU@LB@3'-UUU...AACCG UCUCC...ACA-5'@LB@ \| \|@LB@ 58 50@LB@@LB@@LB@Energy -4.98 kcal/mol@LB@Hybridization Energy -9.02345 kcal/mol@LB@Unfolding Energy - mRNA 1.32881 kcal/mol@LB@Unfolding Energy - sRNA 2.71582 kcal/mol@LB@@LB@Position - mRNA 224 -- 230@LB@Position - sRNA 51 -- 57@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 51 -- 57@LB@
187	0.03882	0.6177	b0403	malZ	-7.79	0.114240	189 -- 197	42 -- 50	maltodextrin glucosidase	_____________188_______198\n_____________\|_________\|\n5'-UUU...AUCAC_________AUGAU...AGC-3'\n______________AGGGGAAUU\n______________\|\|:\|\|\|\|\|\|\n______________UCUCCUUAA\n3'-UUU...CAGUU_________AGUAA...ACA-5'\n_____________\|_________\|\n_____________51________41\n	191 -- 197	42 -- 48	-10.7884 kcal/mol	2.13721 kcal/mol	0.856185 kcal/mol	188 198@LB@ \| \|@LB@5'-UUU...AUCAC AUGAU...AGC-3'@LB@ AGGGGAAUU@LB@ \|\|:\|\|\|\|\|\|@LB@ UCUCCUUAA@LB@3'-UUU...CAGUU AGUAA...ACA-5'@LB@ \| \|@LB@ 51 41@LB@@LB@@LB@Energy -7.79 kcal/mol@LB@Hybridization Energy -10.7884 kcal/mol@LB@Unfolding Energy - mRNA 2.13721 kcal/mol@LB@Unfolding Energy - sRNA 0.856185 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 42 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 42 -- 48@LB@
188	0.03926	0.6177	b4547	ypfN	-8.44	0.084930	187 -- 194	44 -- 51	putative membrane protein UPF0370 family	_____________186______195\n_____________\|________\|\n5'-UGA...UCUGC________AUAAG...AGA-3'\n______________AAGAGGAA\n______________\|\|\|\|\|\|\|\|\n______________UUCUCCUU\n3'-UUU...GCAGU________AAAGU...ACA-5'\n_____________\|________\|\n_____________52_______43\n	188 -- 194	44 -- 50	-10.245 kcal/mol	0.953219 kcal/mol	0.848077 kcal/mol	186 195@LB@ \| \|@LB@5'-UGA...UCUGC AUAAG...AGA-3'@LB@ AAGAGGAA@LB@ \|\|\|\|\|\|\|\|@LB@ UUCUCCUU@LB@3'-UUU...GCAGU AAAGU...ACA-5'@LB@ \| \|@LB@ 52 43@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -10.245 kcal/mol@LB@Unfolding Energy - mRNA 0.953219 kcal/mol@LB@Unfolding Energy - sRNA 0.848077 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 44 -- 51@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
189	0.03933	0.6177	b2461	eutP	-9.78	0.045635	227 -- 240	44 -- 56	putative P-loop NTPase ethanolamine utilization protein	_____________226____________241\n_____________\|______________\|\n5'-AAA...GGUAG________C_____AAACA...CCG-3'\n______________CGUCGGGG_AGGAA\n______________\|\|\|\|:::\|_\|\|\|\|\|\n______________GCAGUUUC_UCCUU\n3'-UUU...ACCGG______________AAAGU...ACA-5'\n_____________\|______________\|\n_____________57_____________43\n	228 -- 234	49 -- 55	-15.0697 kcal/mol	4.34178 kcal/mol	0.948902 kcal/mol	226 241@LB@ \| \|@LB@5'-AAA...GGUAG C AAACA...CCG-3'@LB@ CGUCGGGG AGGAA@LB@ \|\|\|\|:::\| \|\|\|\|\|@LB@ GCAGUUUC UCCUU@LB@3'-UUU...ACCGG AAAGU...ACA-5'@LB@ \| \|@LB@ 57 43@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -15.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.34178 kcal/mol@LB@Unfolding Energy - sRNA 0.948902 kcal/mol@LB@@LB@Position - mRNA 227 -- 240@LB@Position - sRNA 44 -- 56@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 49 -- 55@LB@
190	0.03948	0.6177	b2914	rpiA	-5.25	0.339968	76 -- 83	45 -- 52	ribose 5-phosphate isomerase constitutive	_____________75_______84\n_____________\|________\|\n5'-GAA...GGGCG________UGCCU...CAC-3'\n______________AAAGGGGA\n______________\|\|\|\|:\|\|\|\n______________UUUCUCCU\n3'-UUU...GGCAG________UAAAG...ACA-5'\n_____________\|________\|\n_____________53_______44\n	77 -- 83	45 -- 51	-8.77639 kcal/mol	2.67801 kcal/mol	0.850469 kcal/mol	75 84@LB@ \| \|@LB@5'-GAA...GGGCG UGCCU...CAC-3'@LB@ AAAGGGGA@LB@ \|\|\|\|:\|\|\|@LB@ UUUCUCCU@LB@3'-UUU...GGCAG UAAAG...ACA-5'@LB@ \| \|@LB@ 53 44@LB@@LB@@LB@Energy -5.25 kcal/mol@LB@Hybridization Energy -8.77639 kcal/mol@LB@Unfolding Energy - mRNA 2.67801 kcal/mol@LB@Unfolding Energy - sRNA 0.850469 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 45 -- 52@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 45 -- 51@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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