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
161	0.01187	0.2504	b0093	ftsQ	-14.15	0.043981	32 -- 43	18 -- 29	divisome assembly protein membrane anchored protein involved in growth of wall at septum	_____________31___________44\n_____________\|____________\|\n5'-GCU...GCAAA____________AUUGA...CCG-3'\n______________GGAUGGGGACGU\n______________::\|\|\|\|\|\|\|\|:\|\n______________UUUACCCCUGUA\n3'-UUU...GGUGU____________GUUUC...CCG-5'\n_____________\|____________\|\n_____________30___________17\n	37 -- 43	18 -- 24	-18.9266 kcal/mol	4.11166 kcal/mol	0.665542 kcal/mol	31 44@LB@ \| \|@LB@5'-GCU...GCAAA AUUGA...CCG-3'@LB@ GGAUGGGGACGU@LB@ ::\|\|\|\|\|\|\|\|:\|@LB@ UUUACCCCUGUA@LB@3'-UUU...GGUGU GUUUC...CCG-5'@LB@ \| \|@LB@ 30 17@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -18.9266 kcal/mol@LB@Unfolding Energy - mRNA 4.11166 kcal/mol@LB@Unfolding Energy - sRNA 0.665542 kcal/mol@LB@@LB@Position - mRNA 32 -- 43@LB@Position - sRNA 18 -- 29@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 18 -- 24@LB@
27	0.001238	0.1512	b4045	yjbJ	-9.99	0.275707	259 -- 267	19 -- 28	stress-induced protein UPF0337 family	_____________258________268\n_____________\|__________\|\n5'-CGU...AGAGC__________AACUG...AAG-3'\n______________AAUGGGG_CA\n______________\|\|\|\|\|\|\|_\|\|\n______________UUACCCC_GU\n3'-UUU...GUGUU_______U__AGUUU...CCG-5'\n_____________\|__________\|\n_____________29_________18\n	259 -- 265	22 -- 28	-11.8839 kcal/mol	1.24365 kcal/mol	0.649553 kcal/mol	258 268@LB@ \| \|@LB@5'-CGU...AGAGC AACUG...AAG-3'@LB@ AAUGGGG CA@LB@ \|\|\|\|\|\|\| \|\|@LB@ UUACCCC GU@LB@3'-UUU...GUGUU U AGUUU...CCG-5'@LB@ \| \|@LB@ 29 18@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -11.8839 kcal/mol@LB@Unfolding Energy - mRNA 1.24365 kcal/mol@LB@Unfolding Energy - sRNA 0.649553 kcal/mol@LB@@LB@Position - mRNA 259 -- 267@LB@Position - sRNA 19 -- 28@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 22 -- 28@LB@
65	0.00343	0.1851	b4363	yjjB	-10.89	0.196296	181 -- 193	20 -- 32	DUF3815 family inner membrane protein	_____________180___________194\n_____________\|_____________\|\n5'-ACU...CACUG____UU_______UACGC...GGG-3'\n______________ACGA__UGGGGGC\n______________\|\|:\|__\|\|\|\|\|:\|\n______________UGUU__ACCCCUG\n3'-UUU...CGAGG____UU_______UAGUU...CCG-5'\n_____________\|_____________\|\n_____________33____________19\n	187 -- 193	20 -- 26	-17.0561 kcal/mol	4.01516 kcal/mol	2.14699 kcal/mol	180 194@LB@ \| \|@LB@5'-ACU...CACUG UU UACGC...GGG-3'@LB@ ACGA UGGGGGC@LB@ \|\|:\| \|\|\|\|\|:\|@LB@ UGUU ACCCCUG@LB@3'-UUU...CGAGG UU UAGUU...CCG-5'@LB@ \| \|@LB@ 33 19@LB@@LB@@LB@Energy -10.89 kcal/mol@LB@Hybridization Energy -17.0561 kcal/mol@LB@Unfolding Energy - mRNA 4.01516 kcal/mol@LB@Unfolding Energy - sRNA 2.14699 kcal/mol@LB@@LB@Position - mRNA 181 -- 193@LB@Position - sRNA 20 -- 32@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 20 -- 26@LB@
171	0.01235	0.2504	b1092	fabD	-9.75	0.300248	258 -- 270	47 -- 59	malonyl-CoA-[acyl-carrier-protein] transacylase	_____________257___________271\n_____________\|_____________\|\n5'-AAC...UGCUG_____U_______CGAGC...UUG-3'\n______________GCUGA_AUGGCGG\n______________:\|:\|\|_\|\|\|\|\|\|\|\n______________UGGCU_UACCGCC\n3'-UUU...GAACU_____U_______CCAAC...CCG-5'\n_____________\|_____________\|\n_____________60____________46\n	264 -- 270	47 -- 53	-17.9053 kcal/mol	4.19285 kcal/mol	3.96442 kcal/mol	257 271@LB@ \| \|@LB@5'-AAC...UGCUG U CGAGC...UUG-3'@LB@ GCUGA AUGGCGG@LB@ :\|:\|\| \|\|\|\|\|\|\|@LB@ UGGCU UACCGCC@LB@3'-UUU...GAACU U CCAAC...CCG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -17.9053 kcal/mol@LB@Unfolding Energy - mRNA 4.19285 kcal/mol@LB@Unfolding Energy - sRNA 3.96442 kcal/mol@LB@@LB@Position - mRNA 258 -- 270@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 47 -- 53@LB@
10	0.0003274	0.1087	b1020	phoH	-9.93	0.281763	74 -- 85	48 -- 59	ATP-binding protein; putative PhoH family P-loop ATPase	_____________73___________86\n_____________\|____________\|\n5'-AAU...AUGUC____________UUUUA...AAC-3'\n______________ACUGAAAUGGUG\n______________\|\|:\|\|\|\|\|\|\|:\|\n______________UGGCUUUACCGC\n3'-UUU...GAACU____________CCCAA...CCG-5'\n_____________\|____________\|\n_____________60___________47\n	79 -- 85	48 -- 54	-17.134 kcal/mol	3.24305 kcal/mol	3.96136 kcal/mol	73 86@LB@ \| \|@LB@5'-AAU...AUGUC UUUUA...AAC-3'@LB@ ACUGAAAUGGUG@LB@ \|\|:\|\|\|\|\|\|\|:\|@LB@ UGGCUUUACCGC@LB@3'-UUU...GAACU CCCAA...CCG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -17.134 kcal/mol@LB@Unfolding Energy - mRNA 3.24305 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 74 -- 85@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 48 -- 54@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@
124	0.008958	0.2491	b0124	gcd	-13.85	0.051383	179 -- 193	48 -- 62	glucose dehydrogenase	_____________178_____________194\n_____________\|_______________\|\n5'-UAA...AUUAA_______________UCUCU...GGC-3'\n______________UGAAUUGAAAUGGUG\n______________\|\|\|\|::\|\|\|\|\|\|\|:\|\n______________ACUUGGCUUUACCGC\n3'-UUU...UUGGA_______________CCCAA...CCG-5'\n_____________\|_______________\|\n_____________63______________47\n	187 -- 193	48 -- 54	-20.4838 kcal/mol	2.67361 kcal/mol	3.96136 kcal/mol	178 194@LB@ \| \|@LB@5'-UAA...AUUAA UCUCU...GGC-3'@LB@ UGAAUUGAAAUGGUG@LB@ \|\|\|\|::\|\|\|\|\|\|\|:\|@LB@ ACUUGGCUUUACCGC@LB@3'-UUU...UUGGA CCCAA...CCG-5'@LB@ \| \|@LB@ 63 47@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -20.4838 kcal/mol@LB@Unfolding Energy - mRNA 2.67361 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 179 -- 193@LB@Position - sRNA 48 -- 62@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 48 -- 54@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@
194	0.01408	0.2529	b0952	pqiC	-11.52	0.151794	181 -- 195	48 -- 61	DUF330 family putative lipoprotein	_____________180_____________196\n_____________\|_______________\|\n5'-ACG...AUCCA_________AG____AAACA...GCG-3'\n______________GAGCCGAAG__GGCG\n______________\|\|:\|\|\|\|\|:__\|\|\|\|\n______________CUUGGCUUU__CCGC\n3'-UUU...UGGAA_________A_____CCCAA...CCG-5'\n_____________\|_______________\|\n_____________62______________47\n	183 -- 189	53 -- 59	-21.1549 kcal/mol	5.66908 kcal/mol	3.96136 kcal/mol	180 196@LB@ \| \|@LB@5'-ACG...AUCCA AG AAACA...GCG-3'@LB@ GAGCCGAAG GGCG@LB@ \|\|:\|\|\|\|\|: \|\|\|\|@LB@ CUUGGCUUU CCGC@LB@3'-UUU...UGGAA A CCCAA...CCG-5'@LB@ \| \|@LB@ 62 47@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -21.1549 kcal/mol@LB@Unfolding Energy - mRNA 5.66908 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 181 -- 195@LB@Position - sRNA 48 -- 61@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 53 -- 59@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@

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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching