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
199	0.01447	0.2552	b2790	yqcA	-9.70	0.305430	160 -- 205	1 -- 31	short-chain flavodoxin FMN-binding		_____________159_____________________________________________206\n_____________\|_______________________________________________\|\n5'-CUA...CGGGU________A__G__AAGUUCCUAAUC________AAAC_________GGAAA...CAA-3'\n______________CAGGAUGG_GA_AU____________CAGGGAGA____GGUA_UGGC\n______________\|\|::\|\|\|\|_\|\|_\|\|____________\|\|::\|\|:\|____:\|:\|_\|\|\|\|\n______________GUUUUACC_CU_UA____________GUUUCUUU____UCGU_ACCG\n3'-UUU...GAGGU________C__G______________________________C____-5'\n_____________\|______________________________________________\|\n_____________32_____________________________________________1\n	187 -- 193	10 -- 16	-23.6635 kcal/mol	11.4257 kcal/mol	2.53929 kcal/mol	159 206@LB@ \| \|@LB@5'-CUA...CGGGU A G AAGUUCCUAAUC AAAC GGAAA...CAA-3'@LB@ CAGGAUGG GA AU CAGGGAGA GGUA UGGC@LB@ \|\|::\|\|\|\| \|\| \|\| \|\|::\|\|:\| :\|:\| \|\|\|\|@LB@ GUUUUACC CU UA GUUUCUUU UCGU ACCG@LB@3'-UUU...GAGGU C G C -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -23.6635 kcal/mol@LB@Unfolding Energy - mRNA 11.4257 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 160 -- 205@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 10 -- 16@LB@
76	0.004413	0.2038	b3211	yhcC	-9.63	0.312909	148 -- 162	49 -- 62	putative Fe-S oxidoreductase Radical SAM superfamily protein		_____________147_____________163\n_____________\|_______________\|\n5'-UGC...CGAAU______AA_______AGGCU...GCC-3'\n______________UGAGCU__AAAUGGC\n______________\|\|\|:\|:__\|\|\|\|\|\|\|\n______________ACUUGG__UUUACCG\n3'-UUU...UUGGA______C________CCCCA...CCG-5'\n_____________\|_______________\|\n_____________63______________48\n	156 -- 162	49 -- 55	-15.5959 kcal/mol	2.00852 kcal/mol	3.95968 kcal/mol	147 163@LB@ \| \|@LB@5'-UGC...CGAAU AA AGGCU...GCC-3'@LB@ UGAGCU AAAUGGC@LB@ \|\|\|:\|: \|\|\|\|\|\|\|@LB@ ACUUGG UUUACCG@LB@3'-UUU...UUGGA C CCCCA...CCG-5'@LB@ \| \|@LB@ 63 48@LB@@LB@@LB@Energy -9.63 kcal/mol@LB@Hybridization Energy -15.5959 kcal/mol@LB@Unfolding Energy - mRNA 2.00852 kcal/mol@LB@Unfolding Energy - sRNA 3.95968 kcal/mol@LB@@LB@Position - mRNA 148 -- 162@LB@Position - sRNA 49 -- 62@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 49 -- 55@LB@
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@
156	0.01139	0.2504	b0197	metQ	-9.46	0.330846	169 -- 205	1 -- 33	DL-methionine transporter subunit		_____________168_____________________________________206\n_____________\|_______________________________________\|\n5'-GUG...UUCAA_____CAUAAAUA___________GAAUAA_________GUUCA...UUA-3'\n______________CACAA_________AUUGAAGAAG______GGUA_UGGC\n______________\|\|\|\|\|_________\|\|::\|\|\|\|\|:______:\|:\|_\|\|\|\|\n______________GUGUU_________UAGUUUCUUU______UCGU_ACCG\n3'-UUU...CCGAG_____UUACCCCUG____________________C____-5'\n_____________\|______________________________________\|\n_____________34_____________________________________1\n	185 -- 191	10 -- 16	-16.9822 kcal/mol	4.44131 kcal/mol	3.07861 kcal/mol	168 206@LB@ \| \|@LB@5'-GUG...UUCAA CAUAAAUA GAAUAA GUUCA...UUA-3'@LB@ CACAA AUUGAAGAAG GGUA UGGC@LB@ \|\|\|\|\| \|\|::\|\|\|\|\|: :\|:\| \|\|\|\|@LB@ GUGUU UAGUUUCUUU UCGU ACCG@LB@3'-UUU...CCGAG UUACCCCUG C -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -16.9822 kcal/mol@LB@Unfolding Energy - mRNA 4.44131 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 169 -- 205@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 10 -- 16@LB@
98	0.006107	0.2179	b3822	recQ	-9.35	0.343777	185 -- 205	1 -- 22	ATP-dependent DNA helicase		_____________184_____________________206\n_____________\|_______________________\|\n5'-CGC...UUUCA___A_______U___U_______GCAGG...UUA-3'\n______________GGC_AUCGGGG_GAA___GUGGC\n______________\|:\|_\|\|\|:::\|_:\|\|___\|\|\|\|\|\n______________CUG_UAGUUUC_UUU___CACCG\n3'-UUU...UACCC___________U___CGU_____-5'\n_____________\|______________________\|\n_____________23_____________________1\n	189 -- 195	13 -- 19	-17.8698 kcal/mol	6.98341 kcal/mol	1.54023 kcal/mol	184 206@LB@ \| \|@LB@5'-CGC...UUUCA A U U GCAGG...UUA-3'@LB@ GGC AUCGGGG GAA GUGGC@LB@ \|:\| \|\|\|:::\| :\|\| \|\|\|\|\|@LB@ CUG UAGUUUC UUU CACCG@LB@3'-UUU...UACCC U CGU -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -17.8698 kcal/mol@LB@Unfolding Energy - mRNA 6.98341 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 185 -- 205@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 13 -- 19@LB@
164	0.01206	0.2504	b0882	clpA	-9.12	0.369525	95 -- 107	48 -- 60	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity		_____________94____________108\n_____________\|_____________\|\n5'-UUU...GCAGA____A________AUGGU...CGC-3'\n______________AACC_AAGUGGCG\n______________\|\|\|\|_\|\|:\|\|\|\|\|\n______________UUGG_UUUACCGC\n3'-UUU...GGAAC____C________CCCAA...CCG-5'\n_____________\|_____________\|\n_____________61____________47\n	101 -- 107	48 -- 54	-16.8445 kcal/mol	3.76103 kcal/mol	3.96136 kcal/mol	94 108@LB@ \| \|@LB@5'-UUU...GCAGA A AUGGU...CGC-3'@LB@ AACC AAGUGGCG@LB@ \|\|\|\| \|\|:\|\|\|\|\|@LB@ UUGG UUUACCGC@LB@3'-UUU...GGAAC C CCCAA...CCG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -16.8445 kcal/mol@LB@Unfolding Energy - mRNA 3.76103 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 95 -- 107@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 48 -- 54@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@
80	0.004856	0.213	b1478	adhP	-8.37	0.463200	263 -- 276	48 -- 59	ethanol-active dehydrogenase/acetaldehyde-active reductase		_____________262____________277\n_____________\|______________\|\n5'-GCA...CGCUC_______CA_____AAGCC...GUU-3'\n______________ACUGAAA__UGGCG\n______________\|\|:\|\|\|\|__\|\|\|\|\|\n______________UGGCUUU__ACCGC\n3'-UUU...GAACU______________CCCAA...CCG-5'\n_____________\|______________\|\n_____________60_____________47\n	263 -- 269	53 -- 59	-14.4135 kcal/mol	2.08604 kcal/mol	3.96136 kcal/mol	262 277@LB@ \| \|@LB@5'-GCA...CGCUC CA AAGCC...GUU-3'@LB@ ACUGAAA UGGCG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ UGGCUUU ACCGC@LB@3'-UUU...GAACU CCCAA...CCG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -14.4135 kcal/mol@LB@Unfolding Energy - mRNA 2.08604 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 263 -- 276@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 53 -- 59@LB@
28	0.001242	0.1512	b0879	macB	-8.34	0.466885	135 -- 159	1 -- 22	macrolide ABC transporter peremase/ATPase		_____________134_________________________160\n_____________\|___________________________\|\n5'-AAU...GUUGA__U_________GCUU___________GAUGA...CGG-3'\n______________GA_UGUCAAAGG____GAAGC_G_GGC\n______________\|\|_::\|\|\|\|\|\|:____:\|\|\|\|_\|_\|\|\|\n______________CU_GUAGUUUCU____UUUCG_C_CCG\n3'-UUU...UACCC_____________________U_A___-5'\n_____________\|__________________________\|\n_____________23_________________________1\n	140 -- 146	12 -- 18	-17.2972 kcal/mol	7.41924 kcal/mol	1.54023 kcal/mol	134 160@LB@ \| \|@LB@5'-AAU...GUUGA U GCUU GAUGA...CGG-3'@LB@ GA UGUCAAAGG GAAGC G GGC@LB@ \|\| ::\|\|\|\|\|\|: :\|\|\|\| \| \|\|\|@LB@ CU GUAGUUUCU UUUCG C CCG@LB@3'-UUU...UACCC U A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -8.34 kcal/mol@LB@Hybridization Energy -17.2972 kcal/mol@LB@Unfolding Energy - mRNA 7.41924 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 135 -- 159@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 12 -- 18@LB@
155	0.01136	0.2504	b2168	fruK	-7.75	0.545043	91 -- 105	7 -- 22	fructose-1-phosphate kinase		_____________90_______________106\n_____________\|________________\|\n5'-AAA...CACUU________________CAUCG...CCA-3'\n______________GGCGUU_AAGAAAGGU\n______________\|:\|:\|:_\|\|\|\|\|\|:\|:\n______________CUGUAG_UUCUUUUCG\n3'-UUU...UACCC______U_________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	99 -- 105	7 -- 13	-14.0922 kcal/mol	5.75103 kcal/mol	0.590875 kcal/mol	90 106@LB@ \| \|@LB@5'-AAA...CACUU CAUCG...CCA-3'@LB@ GGCGUU AAGAAAGGU@LB@ \|:\|:\|: \|\|\|\|\|\|:\|:@LB@ CUGUAG UUCUUUUCG@LB@3'-UUU...UACCC U UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -7.75 kcal/mol@LB@Hybridization Energy -14.0922 kcal/mol@LB@Unfolding Energy - mRNA 5.75103 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 91 -- 105@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 7 -- 13@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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