Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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	Additional homologs
143	0.01049	0.2504	b1004	wrbA	-9.61	0.314473	272 -- 293	1 -- 25	NAD(P)H:quinone oxidoreductase		_____________271________________________294\n_____________\|__________________________\|\n5'-UUA...GCUGA___U_________C_______A____GCUGAAG-3'\n______________GGG_GCA____AG_AAAGUGG_UGGC\n______________\|\|\|_:\|\|____\|\|_\|\|\|\|::\|_\|\|\|\|\n______________CCC_UGU____UC_UUUCGUC_ACCG\n3'-UUU...UUUUA___C___AGUU__U____________-5'\n_____________\|_________________________\|\n_____________26________________________1\n	282 -- 288	5 -- 11	-20.1219 kcal/mol	7.99134 kcal/mol	2.51748 kcal/mol	271 294@LB@ \| \|@LB@5'-UUA...GCUGA U C A GCUGAAG-3'@LB@ GGG GCA AG AAAGUGG UGGC@LB@ \|\|\| :\|\| \|\| \|\|\|\|::\| \|\|\|\|@LB@ CCC UGU UC UUUCGUC ACCG@LB@3'-UUU...UUUUA C AGUU U -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -20.1219 kcal/mol@LB@Unfolding Energy - mRNA 7.99134 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 272 -- 293@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 5 -- 11@LB@
102	0.006464	0.2224	b3785	wzzE	-10.51	0.228012	146 -- 168	1 -- 22	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein		_____________145_____________________169\n_____________\|_______________________\|\n5'-GCU...ACGCA___UG__U_____UC________AGCCC...UUA-3'\n______________GAC__CG_AGAAA__GUGGUGGC\n______________\|\|\|__\|:_\|\|\|\|\|__\|::\|\|\|\|\|\n______________CUG__GU_UCUUU__CGUCACCG\n3'-UUU...UACCC___UA__U_____U_________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	162 -- 168	1 -- 7	-19.8866 kcal/mol	7.83936 kcal/mol	1.54023 kcal/mol	145 169@LB@ \| \|@LB@5'-GCU...ACGCA UG U UC AGCCC...UUA-3'@LB@ GAC CG AGAAA GUGGUGGC@LB@ \|\|\| \|: \|\|\|\|\| \|::\|\|\|\|\|@LB@ CUG GU UCUUU CGUCACCG@LB@3'-UUU...UACCC UA U U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -19.8866 kcal/mol@LB@Unfolding Energy - mRNA 7.83936 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 146 -- 168@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 1 -- 7@LB@
61	0.00311	0.1789	b0224	yafK	-14.83	0.030578	183 -- 204	1 -- 20	L D-transpeptidase-related protein		_____________182____________________205\n_____________\|______________________\|\n5'-UUA...CGUUU__________U_______AU__GUAAA...AAG-3'\n______________UAUCAAGGAA_AAGCAGU__GC\n______________:\|\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________GUAGUUUCUU_UUCGUCA__CG\n3'-UUU...CCCCU__________________C___-5'\n_____________\|_____________________\|\n_____________21____________________1\n	194 -- 200	4 -- 10	-21.3079 kcal/mol	5.02402 kcal/mol	1.45855 kcal/mol	182 205@LB@ \| \|@LB@5'-UUA...CGUUU U AU GUAAA...AAG-3'@LB@ UAUCAAGGAA AAGCAGU GC@LB@ :\|\|\|\|\|:\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GUAGUUUCUU UUCGUCA CG@LB@3'-UUU...CCCCU C -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -14.83 kcal/mol@LB@Hybridization Energy -21.3079 kcal/mol@LB@Unfolding Energy - mRNA 5.02402 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 183 -- 204@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 4 -- 10@LB@
96	0.005909	0.216	b0511	ybbW	-13.57	0.059054	201 -- 236	1 -- 27	putative allantoin transporter		_____________200___________________________________237\n_____________\|_____________________________________\|\n5'-UGG...GAUUU____A_____________ACUAUUCC____AC_C___UAUAG...UUA-3'\n______________AUGG__ACAUCAGAGAAA________AGCA__G_GGC\n______________\|\|\|\|__\|\|\|\|\|\|:\|\|\|\|\|________\|\|\|\|__\|_\|\|\|\n______________UACC__UGUAGUUUCUUU________UCGU__C_CCG\n3'-UUU...UGUUU____CC___________________________A___-5'\n_____________\|____________________________________\|\n_____________28___________________________________1\n	211 -- 217	10 -- 16	-23.7564 kcal/mol	7.66376 kcal/mol	2.51867 kcal/mol	200 237@LB@ \| \|@LB@5'-UGG...GAUUU A ACUAUUCC AC C UAUAG...UUA-3'@LB@ AUGG ACAUCAGAGAAA AGCA G GGC@LB@ \|\|\|\| \|\|\|\|\|\|:\|\|\|\|\| \|\|\|\| \| \|\|\|@LB@ UACC UGUAGUUUCUUU UCGU C CCG@LB@3'-UUU...UGUUU CC A -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -23.7564 kcal/mol@LB@Unfolding Energy - mRNA 7.66376 kcal/mol@LB@Unfolding Energy - sRNA 2.51867 kcal/mol@LB@@LB@Position - mRNA 201 -- 236@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 10 -- 16@LB@
106	0.007048	0.2333	b4512	ybdD	-9.12	0.369799	33 -- 54	1 -- 25	DUF466 family protein	b4353	_____________32________________________55\n_____________\|_________________________\|\n5'-GCA...GAGGG___________C___U_________UUAGU...GGG-3'\n______________GGGGAUGUUGG_GAA__GU__UGGC\n______________\|\|\|\|\|::\|:::_\|\|\|__\|:__\|\|\|\|\n______________CCCCUGUAGUU_CUU__CG__ACCG\n3'-UUU...UUUUA___________U___UU__UC____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	36 -- 42	16 -- 22	-21.5624 kcal/mol	9.92515 kcal/mol	2.51748 kcal/mol	32 55@LB@ \| \|@LB@5'-GCA...GAGGG C U UUAGU...GGG-3'@LB@ GGGGAUGUUGG GAA GU UGGC@LB@ \|\|\|\|\|::\|::: \|\|\| \|: \|\|\|\|@LB@ CCCCUGUAGUU CUU CG ACCG@LB@3'-UUU...UUUUA U UU UC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -21.5624 kcal/mol@LB@Unfolding Energy - mRNA 9.92515 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 33 -- 54@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 16 -- 22@LB@
125	0.009022	0.2491	b0658	ybeX	-16.01	0.015431	14 -- 34	5 -- 21	putative ion transport		_____________13____________________35\n_____________\|_____________________\|\n5'-UUA...CGAUC__________UGAC_______AAGAA...ACC-3'\n______________ACAUCGAAGA____GAAGCAG\n______________\|\|\|\|\|:\|\|\|\|____:\|\|\|\|\|\|\n______________UGUAGUUUCU____UUUCGUC\n3'-UUU...ACCCC_____________________ACCG-5'\n_____________\|_____________________\|\n_____________22____________________4\n	28 -- 34	5 -- 11	-20.2475 kcal/mol	2.73159 kcal/mol	1.5073 kcal/mol	13 35@LB@ \| \|@LB@5'-UUA...CGAUC UGAC AAGAA...ACC-3'@LB@ ACAUCGAAGA GAAGCAG@LB@ \|\|\|\|\|:\|\|\|\| :\|\|\|\|\|\|@LB@ UGUAGUUUCU UUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -16.01 kcal/mol@LB@Hybridization Energy -20.2475 kcal/mol@LB@Unfolding Energy - mRNA 2.73159 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 14 -- 34@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 5 -- 11@LB@
51	0.00253	0.1729	b0699	ybfA	-18.06	0.004001	182 -- 204	2 -- 32	DUF2517 family protein		_____________181_____________________________205\n_____________\|_______________________________\|\n5'-AUG...UAGAU_______________________________AACUC...GGA-3'\n______________ACAAAA_GGGG______GAGAAAAGUA_UGG\n______________\|\|\|\|\|\|_\|\|\|\|______:\|\|\|\|\|\|\|:\|_\|\|\|\n______________UGUUUU_CCCC______UUCUUUUCGU_ACC\n3'-UUU...CGAGG______A____UGUAGU__________C___G-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	195 -- 201	6 -- 12	-23.7835 kcal/mol	3.18782 kcal/mol	2.53929 kcal/mol	181 205@LB@ \| \|@LB@5'-AUG...UAGAU AACUC...GGA-3'@LB@ ACAAAA GGGG GAGAAAAGUA UGG@LB@ \|\|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|:\| \|\|\|@LB@ UGUUUU CCCC UUCUUUUCGU ACC@LB@3'-UUU...CGAGG A UGUAGU C G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -18.06 kcal/mol@LB@Hybridization Energy -23.7835 kcal/mol@LB@Unfolding Energy - mRNA 3.18782 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 182 -- 204@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 6 -- 12@LB@
97	0.005972	0.2161	b0768	ybhD	-15.34	0.022873	51 -- 78	6 -- 32	putative DNA-binding transcriptional regulator	b2409	_____________50___________________________79\n_____________\|____________________________\|\n5'-CAG...UUAUU____U____UU__________C______UCUCU...CAU-3'\n______________GCGA_AUGG__ACAUUAAGGG_AAAGCA\n______________:\|:\|_\|\|\|\|__\|\|\|\|:\|\|:\|:_\|\|\|\|\|\|\n______________UGUU_UACC__UGUAGUUUCU_UUUCGU\n3'-UUU...CGAGG____U____CC_________________CACCG-5'\n_____________\|____________________________\|\n_____________33___________________________5\n	64 -- 70	13 -- 19	-24.2506 kcal/mol	6.37495 kcal/mol	2.53457 kcal/mol	50 79@LB@ \| \|@LB@5'-CAG...UUAUU U UU C UCUCU...CAU-3'@LB@ GCGA AUGG ACAUUAAGGG AAAGCA@LB@ :\|:\| \|\|\|\| \|\|\|\|:\|\|:\|: \|\|\|\|\|\|@LB@ UGUU UACC UGUAGUUUCU UUUCGU@LB@3'-UUU...CGAGG U CC CACCG-5'@LB@ \| \|@LB@ 33 5@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -24.2506 kcal/mol@LB@Unfolding Energy - mRNA 6.37495 kcal/mol@LB@Unfolding Energy - sRNA 2.53457 kcal/mol@LB@@LB@Position - mRNA 51 -- 78@LB@Position - sRNA 6 -- 32@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 13 -- 19@LB@
41	0.002071	0.1648	b0992	yccM	-9.88	0.287125	161 -- 167	1 -- 7	putative 4Fe-4S membrane protein		_____________160_____168\n_____________\|_______\|\n5'-AUC...UAGAA_______AUUUG...AAG-3'\n______________UAGUGGC\n______________:\|\|\|\|\|\|\n______________GUCACCG\n3'-UUU...UUUUC_______-5'\n_____________\|______\|\n_____________8______1\n	161 -- 167	1 -- 7	-11.7646 kcal/mol	0.660682 kcal/mol	1.22779 kcal/mol	160 168@LB@ \| \|@LB@5'-AUC...UAGAA AUUUG...AAG-3'@LB@ UAGUGGC@LB@ :\|\|\|\|\|\|@LB@ GUCACCG@LB@3'-UUU...UUUUC -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -11.7646 kcal/mol@LB@Unfolding Energy - mRNA 0.660682 kcal/mol@LB@Unfolding Energy - sRNA 1.22779 kcal/mol@LB@@LB@Position - mRNA 161 -- 167@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 1 -- 7@LB@
42	0.002133	0.1648	b0968	yccX	-12.44	0.101807	184 -- 198	5 -- 23	weak acylphosphatase		_____________183_________________199\n_____________\|___________________\|\n5'-GGC...AUUAA___________________CAAUG...CCG-3'\n______________GGAUA____AGGAGAGCAG\n______________\|\|\|:\|____\|\|:\|:\|\|\|\|\|\n______________CCUGU____UCUUUUCGUC\n3'-UUU...UUACC_____AGUU__________ACCG-5'\n_____________\|___________________\|\n_____________24__________________4\n	192 -- 198	5 -- 11	-17.1825 kcal/mol	3.17176 kcal/mol	1.57523 kcal/mol	183 199@LB@ \| \|@LB@5'-GGC...AUUAA CAAUG...CCG-3'@LB@ GGAUA AGGAGAGCAG@LB@ \|\|\|:\| \|\|:\|:\|\|\|\|\|@LB@ CCUGU UCUUUUCGUC@LB@3'-UUU...UUACC AGUU ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -17.1825 kcal/mol@LB@Unfolding Energy - mRNA 3.17176 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 184 -- 198@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@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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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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