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	Additional homologs
151	0.03043	0.6177	b3081	fadH	-8.56	0.080347	290 -- 297	43 -- 50	2 4-dienoyl-CoA reductase NADH and FMN-linked		_____________289______298\n_____________\|________\|\n5'-UGG...GGGCU________ACC-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	291 -- 297	43 -- 49	-10.5858 kcal/mol	1.17616 kcal/mol	0.845564 kcal/mol	289 298@LB@ \| \|@LB@5'-UGG...GGGCU ACC-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -10.5858 kcal/mol@LB@Unfolding Energy - mRNA 1.17616 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 43 -- 49@LB@
152	0.03059	0.6177	b2609	rpsP	-6.70	0.186060	187 -- 203	23 -- 53	30S ribosomal subunit protein S16		_____________186______________________________204\n_____________\|________________________________\|\n5'-UCA...AUUCA__C_____________________________GUAAC...UCG-3'\n______________CA_AAGAGGA_______________UGUUAUG\n______________\|\|_\|\|\|\|\|\|\|_______________\|:\|\|\|\|\|\n______________GU_UUCUCCU_______________AUAAUAC\n3'-UUU...GGGCA__________UAAAGUAAAAAAAUA_______GGCAG...ACA-5'\n_____________\|________________________________\|\n_____________54_______________________________22\n	197 -- 203	23 -- 29	-10.7305 kcal/mol	2.84664 kcal/mol	1.18482 kcal/mol	186 204@LB@ \| \|@LB@5'-UCA...AUUCA C GUAAC...UCG-3'@LB@ CA AAGAGGA UGUUAUG@LB@ \|\| \|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ GU UUCUCCU AUAAUAC@LB@3'-UUU...GGGCA UAAAGUAAAAAAAUA GGCAG...ACA-5'@LB@ \| \|@LB@ 54 22@LB@@LB@@LB@Energy -6.70 kcal/mol@LB@Hybridization Energy -10.7305 kcal/mol@LB@Unfolding Energy - mRNA 2.84664 kcal/mol@LB@Unfolding Energy - sRNA 1.18482 kcal/mol@LB@@LB@Position - mRNA 187 -- 203@LB@Position - sRNA 23 -- 53@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 23 -- 29@LB@
153	0.03061	0.6177	b4060	yjcB	-6.94	0.167417	88 -- 108	29 -- 50	putative inner membrane protein		_____________87_____________________109\n_____________\|______________________\|\n5'-AUA...CAAAC____U____________G____CUGCA...GGU-3'\n______________AGAG__GUUUCAUUUUU_UGUU\n______________\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|_\|:\|\|\n______________UCUC__UAAAGUAAAAA_AUAA\n3'-UUU...CAGUU____CU___________A____UAAUA...ACA-5'\n_____________\|______________________\|\n_____________51_____________________28\n	97 -- 103	34 -- 40	-13.8913 kcal/mol	5.87088 kcal/mol	1.08007 kcal/mol	87 109@LB@ \| \|@LB@5'-AUA...CAAAC U G CUGCA...GGU-3'@LB@ AGAG GUUUCAUUUUU UGUU@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|\|\| \|:\|\|@LB@ UCUC UAAAGUAAAAA AUAA@LB@3'-UUU...CAGUU CU A UAAUA...ACA-5'@LB@ \| \|@LB@ 51 28@LB@@LB@@LB@Energy -6.94 kcal/mol@LB@Hybridization Energy -13.8913 kcal/mol@LB@Unfolding Energy - mRNA 5.87088 kcal/mol@LB@Unfolding Energy - sRNA 1.08007 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 29 -- 50@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 34 -- 40@LB@
154	0.03071	0.6177	b0368	tauD	-7.18	0.150437	69 -- 85	40 -- 55	taurine dioxygenase 2-oxoglutarate-dependent		_____________68________________86\n_____________\|_________________\|\n5'-GUG...GUUCA_____C___U_______UCGCA...AAC-3'\n______________GUCAG_GGG_GAAUUUC\n______________\|\|\|\|:_\|:\|_\|\|\|\|\|\|\|\n______________CAGUU_CUC_CUUAAAG\n3'-UUU...CCGGG_____U___________UAAAA...ACA-5'\n_____________\|_________________\|\n_____________56________________39\n	79 -- 85	40 -- 46	-16.0696 kcal/mol	7.86965 kcal/mol	1.01784 kcal/mol	68 86@LB@ \| \|@LB@5'-GUG...GUUCA C U UCGCA...AAC-3'@LB@ GUCAG GGG GAAUUUC@LB@ \|\|\|\|: \|:\| \|\|\|\|\|\|\|@LB@ CAGUU CUC CUUAAAG@LB@3'-UUU...CCGGG U UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -16.0696 kcal/mol@LB@Unfolding Energy - mRNA 7.86965 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 69 -- 85@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 40 -- 46@LB@
155	0.03087	0.6177	b1003	yccJ	-9.03	0.064630	130 -- 145	43 -- 56	uncharacterized protein		_____________129______________146\n_____________\|________________\|\n5'-CCU...UUGCU_____UC_________AUGUC...GGU-3'\n______________CGUUA__AAGGGGAAU\n______________\|\|\|:\|__\|\|\|:\|\|\|\|\|\n______________GCAGU__UUCUCCUUA\n3'-UUU...ACCGG________________AAGUA...ACA-5'\n_____________\|________________\|\n_____________57_______________42\n	139 -- 145	43 -- 49	-13.8314 kcal/mol	3.84343 kcal/mol	0.953958 kcal/mol	129 146@LB@ \| \|@LB@5'-CCU...UUGCU UC AUGUC...GGU-3'@LB@ CGUUA AAGGGGAAU@LB@ \|\|\|:\| \|\|\|:\|\|\|\|\|@LB@ GCAGU UUCUCCUUA@LB@3'-UUU...ACCGG AAGUA...ACA-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -13.8314 kcal/mol@LB@Unfolding Energy - mRNA 3.84343 kcal/mol@LB@Unfolding Energy - sRNA 0.953958 kcal/mol@LB@@LB@Position - mRNA 130 -- 145@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 43 -- 49@LB@
156	0.03128	0.6177	b4512	ybdD	-7.87	0.110479	26 -- 38	43 -- 55	DUF466 family protein		_____________25____________39\n_____________\|_____________\|\n5'-GCA...UCAGA__G__________GUUGG...GGG-3'\n______________GU_AGGGGGGGAU\n______________\|\|_\|::\|:\|\|:\|\|\n______________CA_UUUCUCCUUA\n3'-UUU...CCGGG__G__________AAGUA...ACA-5'\n_____________\|_____________\|\n_____________56____________42\n	32 -- 38	43 -- 49	-14.3671 kcal/mol	5.55181 kcal/mol	0.946481 kcal/mol	25 39@LB@ \| \|@LB@5'-GCA...UCAGA G GUUGG...GGG-3'@LB@ GU AGGGGGGGAU@LB@ \|\| \|::\|:\|\|:\|\|@LB@ CA UUUCUCCUUA@LB@3'-UUU...CCGGG G AAGUA...ACA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -7.87 kcal/mol@LB@Hybridization Energy -14.3671 kcal/mol@LB@Unfolding Energy - mRNA 5.55181 kcal/mol@LB@Unfolding Energy - sRNA 0.946481 kcal/mol@LB@@LB@Position - mRNA 26 -- 38@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 43 -- 49@LB@
157	0.03134	0.6177	b4086	alsC	-8.98	0.066369	183 -- 191	45 -- 53	D-allose ABC transporter permease		_____________182_______192\n_____________\|_________\|\n5'-CGC...AUGAG_________GAUUA...CGA-3'\n______________CGAAGAGGA\n______________\|:\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	185 -- 191	45 -- 51	-13.528 kcal/mol	3.63363 kcal/mol	0.917553 kcal/mol	182 192@LB@ \| \|@LB@5'-CGC...AUGAG GAUUA...CGA-3'@LB@ CGAAGAGGA@LB@ \|:\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -13.528 kcal/mol@LB@Unfolding Energy - mRNA 3.63363 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 183 -- 191@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 45 -- 51@LB@
158	0.03174	0.6177	b3185	rpmA	-9.10	0.062717	186 -- 199	39 -- 52	50S ribosomal subunit protein L27		_____________185____________200\n_____________\|______________\|\n5'-GAA...GACCU______A_______AAUGG...CGG-3'\n______________GAGGAG_GAUUUCA\n______________:\|:\|\|\|_:\|\|\|\|\|\|\n______________UUUCUC_UUAAAGU\n3'-UUU...GGCAG______C_______AAAAA...ACA-5'\n_____________\|______________\|\n_____________53_____________38\n	193 -- 199	39 -- 45	-11.8509 kcal/mol	1.7019 kcal/mol	1.05043 kcal/mol	185 200@LB@ \| \|@LB@5'-GAA...GACCU A AAUGG...CGG-3'@LB@ GAGGAG GAUUUCA@LB@ :\|:\|\|\| :\|\|\|\|\|\|@LB@ UUUCUC UUAAAGU@LB@3'-UUU...GGCAG C AAAAA...ACA-5'@LB@ \| \|@LB@ 53 38@LB@@LB@@LB@Energy -9.10 kcal/mol@LB@Hybridization Energy -11.8509 kcal/mol@LB@Unfolding Energy - mRNA 1.7019 kcal/mol@LB@Unfolding Energy - sRNA 1.05043 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 39 -- 52@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 39 -- 45@LB@
159	0.0318	0.6177	b2532	trmJ	-7.64	0.122614	101 -- 114	44 -- 55	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent		_____________100____________115\n_____________\|______________\|\n5'-CGU...UGGAU________AC____AAACG...UGU-3'\n______________GUUAAAGA__GGGA\n______________\|\|:\|\|\|\|\|__\|\|:\|\n______________CAGUUUCU__CCUU\n3'-UUU...CCGGG______________AAAGU...ACA-5'\n_____________\|______________\|\n_____________56_____________43\n	102 -- 108	48 -- 54	-10.9175 kcal/mol	2.33739 kcal/mol	0.941432 kcal/mol	100 115@LB@ \| \|@LB@5'-CGU...UGGAU AC AAACG...UGU-3'@LB@ GUUAAAGA GGGA@LB@ \|\|:\|\|\|\|\| \|\|:\|@LB@ CAGUUUCU CCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -10.9175 kcal/mol@LB@Unfolding Energy - mRNA 2.33739 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 101 -- 114@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 48 -- 54@LB@
160	0.0322	0.6177	b1550	gnsB	-8.75	0.073686	189 -- 197	44 -- 52	Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts)	b4517	_____________188_______198\n_____________\|_________\|\n5'-UGG...GACUA_________AUGAU...UUA-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	191 -- 197	44 -- 50	-11.5466 kcal/mol	1.93458 kcal/mol	0.860683 kcal/mol	188 198@LB@ \| \|@LB@5'-UGG...GACUA AUGAU...UUA-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -11.5466 kcal/mol@LB@Unfolding Energy - mRNA 1.93458 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@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