Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
188	0.0185	0.3104	b3364	tsgA	-7.52	0.300608	282 -- 299	12 -- 29	putative transporter	_____________281________________300\n_____________\|__________________\|\n5'-CCA...UCACC_____________G____A-3'\n______________GGGAUGGUGAUGG_AAAU\n______________\|\|\|\|\|\|:\|\|\|\|::_\|\|\|\|\n______________CCCUACUACUAUU_UUUA\n3'-UUU...UAAGU_____________G____CGCGC...AAG-5'\n_____________\|__________________\|\n_____________30_________________11\n	282 -- 288	23 -- 29	-23.3156 kcal/mol	8.39977 kcal/mol	7.39774 kcal/mol	281 300@LB@ \| \|@LB@5'-CCA...UCACC G A-3'@LB@ GGGAUGGUGAUGG AAAU@LB@ \|\|\|\|\|\|:\|\|\|\|:: \|\|\|\|@LB@ CCCUACUACUAUU UUUA@LB@3'-UUU...UAAGU G CGCGC...AAG-5'@LB@ \| \|@LB@ 30 11@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -23.3156 kcal/mol@LB@Unfolding Energy - mRNA 8.39977 kcal/mol@LB@Unfolding Energy - sRNA 7.39774 kcal/mol@LB@@LB@Position - mRNA 282 -- 299@LB@Position - sRNA 12 -- 29@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 23 -- 29@LB@
199	0.01944	0.3104	b3657	yicJ	-13.22	0.033173	129 -- 161	8 -- 45	putative transporter	_____________128_____________________________________162\n_____________\|_______________________________________\|\n5'-CAG...GAAUA_________CA_____________UU____A________UAUCG...UGU-3'\n______________UUCG_CUCU_____CAGGGAUGGU____AC_AAAUGCGU\n______________\|\|\|:_\|\|\|\|_____\|\|\|\|\|\|\|\|:\|____\|\|_\|\|\|\|\|\|\|:\n______________AAGU_GAGA_____GUCCCUACUA____UG_UUUACGCG\n3'-UUU...UUUUA____A____CUUAA__________CUAU___________CAGAAAG-5'\n_____________\|_______________________________________\|\n_____________46______________________________________7\n	155 -- 161	8 -- 14	-30.3918 kcal/mol	7.7216 kcal/mol	9.45195 kcal/mol	128 162@LB@ \| \|@LB@5'-CAG...GAAUA CA UU A UAUCG...UGU-3'@LB@ UUCG CUCU CAGGGAUGGU AC AAAUGCGU@LB@ \|\|\|: \|\|\|\| \|\|\|\|\|\|\|\|:\| \|\| \|\|\|\|\|\|\|:@LB@ AAGU GAGA GUCCCUACUA UG UUUACGCG@LB@3'-UUU...UUUUA A CUUAA CUAU CAGAAAG-5'@LB@ \| \|@LB@ 46 7@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -30.3918 kcal/mol@LB@Unfolding Energy - mRNA 7.7216 kcal/mol@LB@Unfolding Energy - sRNA 9.45195 kcal/mol@LB@@LB@Position - mRNA 129 -- 161@LB@Position - sRNA 8 -- 45@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 8 -- 14@LB@
42	0.002847	0.2296	b1638	pdxH	-9.07	0.172497	29 -- 35	5 -- 11	pyridoxine 5'-phosphate oxidase	_____________28______36\n_____________\|_______\|\n5'-UCU...CUGGC_______ACACU...CCC-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	29 -- 35	5 -- 11	-12.2635 kcal/mol	2.08033 kcal/mol	1.11145 kcal/mol	28 36@LB@ \| \|@LB@5'-UCU...CUGGC ACACU...CCC-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -9.07 kcal/mol@LB@Hybridization Energy -12.2635 kcal/mol@LB@Unfolding Energy - mRNA 2.08033 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 29 -- 35@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 5 -- 11@LB@
162	0.01506	0.3104	b0871	poxB	-6.02	0.481603	228 -- 255	23 -- 53	pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding	_____________227_______________________________256\n_____________\|_________________________________\|\n5'-CCG...AUAUC_____________________CGG_________AACGC...GUG-3'\n______________GCCAAAA___CA_CUC_GAAU___CAGGGGUGA\n______________\|\|\|\|\|\|\|___\|\|_\|\|\|_\|\|\|\|___\|\|\|\|\|:\|\|\|\n______________CGGUUUU___GU_GAG_CUUA___GUCCCUACU\n3'-UUU...CUCAC_______AAA__A___A____A___________ACUAU...AAG-5'\n_____________\|_________________________________\|\n_____________54________________________________22\n	249 -- 255	23 -- 29	-28.0165 kcal/mol	6.84512 kcal/mol	15.1535 kcal/mol	227 256@LB@ \| \|@LB@5'-CCG...AUAUC CGG AACGC...GUG-3'@LB@ GCCAAAA CA CUC GAAU CAGGGGUGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CGGUUUU GU GAG CUUA GUCCCUACU@LB@3'-UUU...CUCAC AAA A A A ACUAU...AAG-5'@LB@ \| \|@LB@ 54 22@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -28.0165 kcal/mol@LB@Unfolding Energy - mRNA 6.84512 kcal/mol@LB@Unfolding Energy - sRNA 15.1535 kcal/mol@LB@@LB@Position - mRNA 228 -- 255@LB@Position - sRNA 23 -- 53@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 23 -- 29@LB@
129	0.01261	0.3104	b3025	qseB	-10.92	0.084347	141 -- 152	5 -- 17	quorum sensing DNA-binding response regulator in two-component regulatory system with QseC	_____________140___________153\n_____________\|_____________\|\n5'-GUG...GCUGU_____________ACAAC...GUC-3'\n______________ACAGA_GCGCGUU\n______________\|\|\|:\|_\|\|\|\|\|\|:\n______________UGUUU_CGCGCAG\n3'-UUU...ACUAU_____A_______AAAG-5'\n_____________\|_____________\|\n_____________18____________4\n	146 -- 152	5 -- 11	-15.7823 kcal/mol	3.63703 kcal/mol	1.22241 kcal/mol	140 153@LB@ \| \|@LB@5'-GUG...GCUGU ACAAC...GUC-3'@LB@ ACAGA GCGCGUU@LB@ \|\|\|:\| \|\|\|\|\|\|:@LB@ UGUUU CGCGCAG@LB@3'-UUU...ACUAU A AAAG-5'@LB@ \| \|@LB@ 18 4@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -15.7823 kcal/mol@LB@Unfolding Energy - mRNA 3.63703 kcal/mol@LB@Unfolding Energy - sRNA 1.22241 kcal/mol@LB@@LB@Position - mRNA 141 -- 152@LB@Position - sRNA 5 -- 17@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 5 -- 11@LB@
123	0.01235	0.3104	b0097	secM	-7.65	0.286972	189 -- 203	7 -- 21	regulator of secA translation	_____________188_____________204\n_____________\|_______________\|\n5'-UGG...AUCGG________UAA____AGUGG...CGC-3'\n______________GAUGGCAA___CGUG\n______________\|\|\|::\|\|\|___\|\|:\|\n______________CUAUUGUU___GCGC\n3'-UUU...UACUA________UAC____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	190 -- 196	14 -- 20	-12.5088 kcal/mol	3.61266 kcal/mol	1.24179 kcal/mol	188 204@LB@ \| \|@LB@5'-UGG...AUCGG UAA AGUGG...CGC-3'@LB@ GAUGGCAA CGUG@LB@ \|\|\|::\|\|\| \|\|:\|@LB@ CUAUUGUU GCGC@LB@3'-UUU...UACUA UAC AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -12.5088 kcal/mol@LB@Unfolding Energy - mRNA 3.61266 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 189 -- 203@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 14 -- 20@LB@
194	0.0191	0.3104	b2698	recX	-10.17	0.113250	93 -- 107	8 -- 22	regulatory protein for RecA	_____________92______________108\n_____________\|_______________\|\n5'-AAA...GUAGA__________G____AGCAG...GAC-3'\n______________UGAUAGCGAA_GCGU\n______________\|\|\|\|\|:\|:\|\|_\|\|\|:\n______________ACUAUUGUUU_CGCG\n3'-UUU...CUACU__________A____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	96 -- 102	13 -- 19	-16.2974 kcal/mol	4.88496 kcal/mol	1.23838 kcal/mol	92 108@LB@ \| \|@LB@5'-AAA...GUAGA G AGCAG...GAC-3'@LB@ UGAUAGCGAA GCGU@LB@ \|\|\|\|\|:\|:\|\| \|\|\|:@LB@ ACUAUUGUUU CGCG@LB@3'-UUU...CUACU A CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -16.2974 kcal/mol@LB@Unfolding Energy - mRNA 4.88496 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 93 -- 107@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 13 -- 19@LB@
17	0.0005644	0.1124	b0949	uup	-13.14	0.034258	282 -- 297	4 -- 21	replication regulatory ABC-F family DNA-binding ATPase	_____________281________________298\n_____________\|__________________\|\n5'-GAU...UCGAA__________________GUC-3'\n______________GAUAACGAA__CGUGUUU\n______________\|\|\|\|\|\|:\|\|__\|\|:\|\|:\|\n______________CUAUUGUUU__GCGCAGA\n3'-UUU...UACUA_________AC_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	291 -- 297	4 -- 10	-16.3224 kcal/mol	1.92683 kcal/mol	1.2552 kcal/mol	281 298@LB@ \| \|@LB@5'-GAU...UCGAA GUC-3'@LB@ GAUAACGAA CGUGUUU@LB@ \|\|\|\|\|\|:\|\| \|\|:\|\|:\|@LB@ CUAUUGUUU GCGCAGA@LB@3'-UUU...UACUA AC AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 1.92683 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 282 -- 297@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 4 -- 10@LB@
164	0.0157	0.3104	b1735	chbR	-6.99	0.357617	139 -- 145	6 -- 12	repressor of chb operon for N N'-diacetylchitobiose utilization	_____________138_____146\n_____________\|_______\|\n5'-GAU...AUGCU_______GAACU...CUG-3'\n______________UGCGCGU\n______________\|\|\|\|\|\|\|\n______________ACGCGCA\n3'-UUU...UGUUU_______GAAAG-5'\n_____________\|_______\|\n_____________13______5\n	139 -- 145	6 -- 12	-12.5358 kcal/mol	4.43858 kcal/mol	1.10371 kcal/mol	138 146@LB@ \| \|@LB@5'-GAU...AUGCU GAACU...CUG-3'@LB@ UGCGCGU@LB@ \|\|\|\|\|\|\|@LB@ ACGCGCA@LB@3'-UUU...UGUUU GAAAG-5'@LB@ \| \|@LB@ 13 5@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -12.5358 kcal/mol@LB@Unfolding Energy - mRNA 4.43858 kcal/mol@LB@Unfolding Energy - sRNA 1.10371 kcal/mol@LB@@LB@Position - mRNA 139 -- 145@LB@Position - sRNA 6 -- 12@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 6 -- 12@LB@
99	0.009943	0.3104	b3405	ompR	-10.46	0.101388	231 -- 245	8 -- 21	response regulator in two-component regulatory system with EnvZ	_____________230_____________246\n_____________\|_______________\|\n5'-AAU...UGGUC________C______CUGCG...GCG-3'\n______________GAUGACGA_AUGCGC\n______________\|\|\|:\|\|:\|_\|\|\|\|\|\|\n______________CUAUUGUU_UACGCG\n3'-UUU...UACUA_______________CAGAAAG-5'\n_____________\|_______________\|\n_____________22______________7\n	232 -- 238	14 -- 20	-17.2341 kcal/mol	5.5408 kcal/mol	1.23638 kcal/mol	230 246@LB@ \| \|@LB@5'-AAU...UGGUC C CUGCG...GCG-3'@LB@ GAUGACGA AUGCGC@LB@ \|\|\|:\|\|:\| \|\|\|\|\|\|@LB@ CUAUUGUU UACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -17.2341 kcal/mol@LB@Unfolding Energy - mRNA 5.5408 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 231 -- 245@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 14 -- 20@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)

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service.

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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