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
150	0.03022	0.6177	b1285	gmr	-9.04	0.064446	208 -- 218	47 -- 57	cyclic-di-GMP phosphodiesterase; csgD regulator; modulator of RNase II stability	_____________207_________219\n_____________\|___________\|\n5'-UUU...GAAAA___________UCCAC...CUA-3'\n______________CCGUUAGGGAG\n______________\|\|\|\|:\|::\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	212 -- 218	47 -- 53	-14.7452 kcal/mol	2.96952 kcal/mol	2.73556 kcal/mol	207 219@LB@ \| \|@LB@5'-UUU...GAAAA UCCAC...CUA-3'@LB@ CCGUUAGGGAG@LB@ \|\|\|\|:\|::\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -14.7452 kcal/mol@LB@Unfolding Energy - mRNA 2.96952 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 208 -- 218@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 47 -- 53@LB@
170	0.03452	0.6177	b0792	ybhR	-7.08	0.157577	208 -- 236	47 -- 69	putative ABC transporter permease	_____________207____________________________237\n_____________\|______________________________\|\n5'-CAG...GUUUC______UA___ACGUUAA____________UUGCA...AGG-3'\n______________AUCGCU__UGG_______UCCG_CAAAGAG\n______________\|\|\|\|\|\|__\|\|\|_______:\|\|\|_\|\|\|\|\|\|\|\n______________UAGCGA__ACC_______GGGC_GUUUCUC\n3'-UUU...GGUUA______UA______________A_______CUUAA...ACA-5'\n_____________\|______________________________\|\n_____________70_____________________________46\n	230 -- 236	47 -- 53	-23.2437 kcal/mol	4.95079 kcal/mol	11.2154 kcal/mol	207 237@LB@ \| \|@LB@5'-CAG...GUUUC UA ACGUUAA UUGCA...AGG-3'@LB@ AUCGCU UGG UCCG CAAAGAG@LB@ \|\|\|\|\|\| \|\|\| :\|\|\| \|\|\|\|\|\|\|@LB@ UAGCGA ACC GGGC GUUUCUC@LB@3'-UUU...GGUUA UA A CUUAA...ACA-5'@LB@ \| \|@LB@ 70 46@LB@@LB@@LB@Energy -7.08 kcal/mol@LB@Hybridization Energy -23.2437 kcal/mol@LB@Unfolding Energy - mRNA 4.95079 kcal/mol@LB@Unfolding Energy - sRNA 11.2154 kcal/mol@LB@@LB@Position - mRNA 208 -- 236@LB@Position - sRNA 47 -- 69@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 47 -- 53@LB@
180	0.03697	0.6177	b1325	ycjG	-6.24	0.226397	189 -- 195	47 -- 53	L-Ala-D/L-Glu epimerase	_____________188_____196\n_____________\|_______\|\n5'-AAG...GACAA_______UAAAG...AAC-3'\n______________CAAGGAG\n______________\|\|\|:\|\|\|\n______________GUUUCUC\n3'-UUU...GGGCA_______CUUAA...ACA-5'\n_____________\|_______\|\n_____________54______46\n	189 -- 195	47 -- 53	-8.11062 kcal/mol	0.981925 kcal/mol	0.886139 kcal/mol	188 196@LB@ \| \|@LB@5'-AAG...GACAA UAAAG...AAC-3'@LB@ CAAGGAG@LB@ \|\|\|:\|\|\|@LB@ GUUUCUC@LB@3'-UUU...GGGCA CUUAA...ACA-5'@LB@ \| \|@LB@ 54 46@LB@@LB@@LB@Energy -6.24 kcal/mol@LB@Hybridization Energy -8.11062 kcal/mol@LB@Unfolding Energy - mRNA 0.981925 kcal/mol@LB@Unfolding Energy - sRNA 0.886139 kcal/mol@LB@@LB@Position - mRNA 189 -- 195@LB@Position - sRNA 47 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 47 -- 53@LB@
191	0.0398	0.6177	b4335	yjiM	-5.72	0.281824	283 -- 290	47 -- 54	putative 2-hydroxyglutaryl-CoA dehydratase	_____________282______291\n_____________\|________\|\n5'-CGG...GGAUC________CGCGG...UUC-3'\n______________UCAAGGAG\n______________\|\|\|\|:\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	284 -- 290	47 -- 53	-8.85878 kcal/mol	2.24401 kcal/mol	0.897871 kcal/mol	282 291@LB@ \| \|@LB@5'-CGG...GGAUC CGCGG...UUC-3'@LB@ UCAAGGAG@LB@ \|\|\|\|:\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -5.72 kcal/mol@LB@Hybridization Energy -8.85878 kcal/mol@LB@Unfolding Energy - mRNA 2.24401 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 283 -- 290@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 47 -- 53@LB@
193	0.04043	0.6177	b1180	ycgM	-6.42	0.210248	289 -- 296	47 -- 54	putative isomerase/hydrolase	_____________288______297\n_____________\|________\|\n5'-GAU...ACAUA________AUGG-3'\n______________UUAAAGAG\n______________\|:\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	290 -- 296	47 -- 53	-7.63974 kcal/mol	0.325787 kcal/mol	0.897871 kcal/mol	288 297@LB@ \| \|@LB@5'-GAU...ACAUA AUGG-3'@LB@ UUAAAGAG@LB@ \|:\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -6.42 kcal/mol@LB@Hybridization Energy -7.63974 kcal/mol@LB@Unfolding Energy - mRNA 0.325787 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 289 -- 296@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 47 -- 53@LB@
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@
52	0.01005	0.6177	b3985	rplJ	-10.76	0.028819	17 -- 26	48 -- 57	50S ribosomal subunit protein L10	_____________16_________27\n_____________\|__________\|\n5'-UGG...GGCCU__________CCGCA...UAA-3'\n______________CCGUCGAAGA\n______________\|\|\|\|\|:\|\|\|\|\n______________GGCAGUUUCU\n3'-UUU...AACCG__________CCUUA...ACA-5'\n_____________\|__________\|\n_____________58_________47\n	20 -- 26	48 -- 54	-14.4896 kcal/mol	0.999171 kcal/mol	2.73483 kcal/mol	16 27@LB@ \| \|@LB@5'-UGG...GGCCU CCGCA...UAA-3'@LB@ CCGUCGAAGA@LB@ \|\|\|\|\|:\|\|\|\|@LB@ GGCAGUUUCU@LB@3'-UUU...AACCG CCUUA...ACA-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -14.4896 kcal/mol@LB@Unfolding Energy - mRNA 0.999171 kcal/mol@LB@Unfolding Energy - sRNA 2.73483 kcal/mol@LB@@LB@Position - mRNA 17 -- 26@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 48 -- 54@LB@
60	0.01286	0.6177	b4113	basR	-8.68	0.076010	6 -- 31	48 -- 75	response regulator in two-component regulatory system with BasS	_____________5____________________________32\n_____________\|____________________________\|\n______5'-CAGGU_______C____________________AUUAU...CGC-3'\n______________GCCGAUG_UGCUG_UGG_CUGUCGGAGG\n______________\|\|\|:\|\|:_:\|\|\|:_\|\|\|_\|:\|\|\|::\|\|:\n______________CGGUUAU_GCGAU_ACC_GGCAGUUUCU\n3'-UUU...UUUAC_______A_____A___G__________CCUUA...ACA-5'\n_____________\|____________________________\|\n_____________76___________________________47\n	25 -- 31	48 -- 54	-31.4034 kcal/mol	11.3837 kcal/mol	11.3355 kcal/mol	5 32@LB@ \| \|@LB@ 5'-CAGGU C AUUAU...CGC-3'@LB@ GCCGAUG UGCUG UGG CUGUCGGAGG@LB@ \|\|\|:\|\|: :\|\|\|: \|\|\| \|:\|\|\|::\|\|:@LB@ CGGUUAU GCGAU ACC GGCAGUUUCU@LB@3'-UUU...UUUAC A A G CCUUA...ACA-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -8.68 kcal/mol@LB@Hybridization Energy -31.4034 kcal/mol@LB@Unfolding Energy - mRNA 11.3837 kcal/mol@LB@Unfolding Energy - sRNA 11.3355 kcal/mol@LB@@LB@Position - mRNA 6 -- 31@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 48 -- 54@LB@
65	0.01408	0.6177	b3176	glmM	-9.74	0.046438	133 -- 141	48 -- 56	phosphoglucosamine mutase	_____________132_______142\n_____________\|_________\|\n5'-GUU...CAUGA_________AACCG...CGG-3'\n______________CGUCAAAGA\n______________\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCU\n3'-UUU...ACCGG_________CCUUA...ACA-5'\n_____________\|_________\|\n_____________57________47\n	135 -- 141	48 -- 54	-11.8395 kcal/mol	1.20122 kcal/mol	0.896433 kcal/mol	132 142@LB@ \| \|@LB@5'-GUU...CAUGA AACCG...CGG-3'@LB@ CGUCAAAGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCU@LB@3'-UUU...ACCGG CCUUA...ACA-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -11.8395 kcal/mol@LB@Unfolding Energy - mRNA 1.20122 kcal/mol@LB@Unfolding Energy - sRNA 0.896433 kcal/mol@LB@@LB@Position - mRNA 133 -- 141@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 48 -- 54@LB@
69	0.01434	0.6177	b0551	quuD	-6.03	0.248082	117 -- 124	48 -- 55	DLP12 prophage; putative antitermination protein	_____________116______125\n_____________\|________\|\n5'-ACU...AUGAA________UAACA...GAU-3'\n______________GUCAGAGA\n______________\|\|\|\|:\|\|\|\n______________CAGUUUCU\n3'-UUU...CCGGG________CCUUA...ACA-5'\n_____________\|________\|\n_____________56_______47\n	118 -- 124	48 -- 54	-9.27195 kcal/mol	2.92769 kcal/mol	0.318869 kcal/mol	116 125@LB@ \| \|@LB@5'-ACU...AUGAA UAACA...GAU-3'@LB@ GUCAGAGA@LB@ \|\|\|\|:\|\|\|@LB@ CAGUUUCU@LB@3'-UUU...CCGGG CCUUA...ACA-5'@LB@ \| \|@LB@ 56 47@LB@@LB@@LB@Energy -6.03 kcal/mol@LB@Hybridization Energy -9.27195 kcal/mol@LB@Unfolding Energy - mRNA 2.92769 kcal/mol@LB@Unfolding Energy - sRNA 0.318869 kcal/mol@LB@@LB@Position - mRNA 117 -- 124@LB@Position - sRNA 48 -- 55@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 48 -- 54@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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