Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
140	0.008117	0.2031	b3221	yhcH	-13.19	0.033484	158 -- 212	34 -- 73	DUF386 family protein cupin superfamily	_____________157_____________________________________________________213\n_____________\|_______________________________________________________\|\n5'-AUC...UGAUG____UUUAC__GG___________UGGCCCAGGGAGAA_______G_________GAAGU...AAG-3'\n______________CAGG_____UU__GGCUGCGCUGU______________AAAUUAU_AUGAUGGGU\n______________\|\|\|\|_____\|:__\|\|\|\|\|\|\|\|:\|\|______________\|\|\|\|\|\|\|_\|\|\|\|\|\|:\|\|\n______________GUCC_____AG__CCGACGCGGCA______________UUUAAUA_UACUACUCA\n3'-UUU...UUGUG____CUUU___AA________________________________A_________AUGUU...GUG-5'\n_____________\|_______________________________________________________\|\n_____________74______________________________________________________33\n	206 -- 212	34 -- 40	-41.3429 kcal/mol	18.8865 kcal/mol	9.26614 kcal/mol	157 213@LB@ \| \|@LB@5'-AUC...UGAUG UUUAC GG UGGCCCAGGGAGAA G GAAGU...AAG-3'@LB@ CAGG UU GGCUGCGCUGU AAAUUAU AUGAUGGGU@LB@ \|\|\|\| \|: \|\|\|\|\|\|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\|\|@LB@ GUCC AG CCGACGCGGCA UUUAAUA UACUACUCA@LB@3'-UUU...UUGUG CUUU AA A AUGUU...GUG-5'@LB@ \| \|@LB@ 74 33@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -41.3429 kcal/mol@LB@Unfolding Energy - mRNA 18.8865 kcal/mol@LB@Unfolding Energy - sRNA 9.26614 kcal/mol@LB@@LB@Position - mRNA 158 -- 212@LB@Position - sRNA 34 -- 73@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 34 -- 40@LB@
190	0.01143	0.2119	b3233	yhcB	-11.72	0.064941	161 -- 178	66 -- 81	DUF1043 family inner membrane-anchored protein	_____________160________________179\n_____________\|__________________\|\n5'-UUU...CUGAA_________CUAC_____CAAAA...CGU-3'\n______________GCCAACACC____GGAAA\n______________\|\|\|\|\|\|\|\|\|____\|\|\|\|\|\n______________CGGUUGUGG____CCUUU\n3'-UUU...UGACG_________UC_______AGAAC...GUG-5'\n_____________\|__________________\|\n_____________82_________________65\n	163 -- 169	73 -- 79	-21.1167 kcal/mol	2.37182 kcal/mol	7.0207 kcal/mol	160 179@LB@ \| \|@LB@5'-UUU...CUGAA CUAC CAAAA...CGU-3'@LB@ GCCAACACC GGAAA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CGGUUGUGG CCUUU@LB@3'-UUU...UGACG UC AGAAC...GUG-5'@LB@ \| \|@LB@ 82 65@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -21.1167 kcal/mol@LB@Unfolding Energy - mRNA 2.37182 kcal/mol@LB@Unfolding Energy - sRNA 7.0207 kcal/mol@LB@@LB@Position - mRNA 161 -- 178@LB@Position - sRNA 66 -- 81@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 73 -- 79@LB@
186	0.01109	0.2089	b3234	degQ	-11.96	0.058310	267 -- 277	3 -- 13	serine endoprotease periplasmic	_____________266_________278\n_____________\|___________\|\n5'-CUG...CGUCA___________CGCGU...UUG-3'\n______________UUUCAGGCCGU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________AAAGUCCGGCG\n3'-UUU...GACAA___________UG-5'\n_____________\|___________\|\n_____________14__________2\n	271 -- 277	3 -- 9	-19.4081 kcal/mol	1.79109 kcal/mol	5.63489 kcal/mol	266 278@LB@ \| \|@LB@5'-CUG...CGUCA CGCGU...UUG-3'@LB@ UUUCAGGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ AAAGUCCGGCG@LB@3'-UUU...GACAA UG-5'@LB@ \| \|@LB@ 14 2@LB@@LB@@LB@Energy -11.96 kcal/mol@LB@Hybridization Energy -19.4081 kcal/mol@LB@Unfolding Energy - mRNA 1.79109 kcal/mol@LB@Unfolding Energy - sRNA 5.63489 kcal/mol@LB@@LB@Position - mRNA 267 -- 277@LB@Position - sRNA 3 -- 13@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 3 -- 9@LB@
39	0.002105	0.1727	b3249	mreD	-13.67	0.026871	102 -- 115	74 -- 87	cell wall structural complex MreBCD transmembrane component MreD	_____________101____________116\n_____________\|______________\|\n5'-CCU...GCGCC______________AGCCU...UUU-3'\n______________UGCUGCGCCGACAC\n______________\|:\|\|\|\|\|\|\|:\|\|\|\|\n______________AUGACGCGGUUGUG\n3'-UUU...CGCUU______________GUCCC...GUG-5'\n_____________\|______________\|\n_____________88_____________73\n	109 -- 115	74 -- 80	-25.8251 kcal/mol	5.39353 kcal/mol	6.75739 kcal/mol	101 116@LB@ \| \|@LB@5'-CCU...GCGCC AGCCU...UUU-3'@LB@ UGCUGCGCCGACAC@LB@ \|:\|\|\|\|\|\|\|:\|\|\|\|@LB@ AUGACGCGGUUGUG@LB@3'-UUU...CGCUU GUCCC...GUG-5'@LB@ \| \|@LB@ 88 73@LB@@LB@@LB@Energy -13.67 kcal/mol@LB@Hybridization Energy -25.8251 kcal/mol@LB@Unfolding Energy - mRNA 5.39353 kcal/mol@LB@Unfolding Energy - sRNA 6.75739 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 74 -- 87@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 74 -- 80@LB@
78	0.004296	0.1855	b3258	panF	-10.37	0.118507	142 -- 153	52 -- 62	pantothenate:sodium symporter	_____________141__________154\n_____________\|____________\|\n5'-GGC...UUUAU___A________GGCGA...UUA-3'\n______________UGG_CUGUGCUG\n______________\|\|\|_\|\|\|:\|\|:\|\n______________ACC_GACGCGGC\n3'-UUU...UUAGA____________AUUUA...GUG-5'\n_____________\|____________\|\n_____________63___________51\n	147 -- 153	52 -- 58	-17.1407 kcal/mol	1.89201 kcal/mol	4.8804 kcal/mol	141 154@LB@ \| \|@LB@5'-GGC...UUUAU A GGCGA...UUA-3'@LB@ UGG CUGUGCUG@LB@ \|\|\| \|\|\|:\|\|:\|@LB@ ACC GACGCGGC@LB@3'-UUU...UUAGA AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -17.1407 kcal/mol@LB@Unfolding Energy - mRNA 1.89201 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 52 -- 58@LB@
173	0.01023	0.2071	b3297	rpsK	-11.54	0.070538	32 -- 43	48 -- 59	30S ribosomal subunit protein S11	_____________31___________44\n_____________\|____________\|\n5'-CGA...GUGAU____________AUCAG...CUA-3'\n______________CUGCGCCGUGAA\n______________\|\|\|\|\|\|\|\|\|:\|\|\n______________GACGCGGCAUUU\n3'-UUU...GAACC____________AAUAA...GUG-5'\n_____________\|____________\|\n_____________60___________47\n	37 -- 43	48 -- 54	-20.6796 kcal/mol	2.9935 kcal/mol	6.14631 kcal/mol	31 44@LB@ \| \|@LB@5'-CGA...GUGAU AUCAG...CUA-3'@LB@ CUGCGCCGUGAA@LB@ \|\|\|\|\|\|\|\|\|:\|\|@LB@ GACGCGGCAUUU@LB@3'-UUU...GAACC AAUAA...GUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -11.54 kcal/mol@LB@Hybridization Energy -20.6796 kcal/mol@LB@Unfolding Energy - mRNA 2.9935 kcal/mol@LB@Unfolding Energy - sRNA 6.14631 kcal/mol@LB@@LB@Position - mRNA 32 -- 43@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 48 -- 54@LB@
81	0.004478	0.1855	b3327	gspF	-8.77	0.233220	243 -- 251	26 -- 34	general secretory pathway component cryptic	_____________242_______252\n_____________\|_________\|\n5'-AUG...AAAAA_________AUCAU...AAG-3'\n______________UUGCAAGGG\n______________\|\|:\|\|\|\|\|\|\n______________AAUGUUCCC\n3'-UUU...UACUC_________GUGUC...GUG-5'\n_____________\|_________\|\n_____________35________25\n	245 -- 251	26 -- 32	-12.3281 kcal/mol	0.874927 kcal/mol	2.67841 kcal/mol	242 252@LB@ \| \|@LB@5'-AUG...AAAAA AUCAU...AAG-3'@LB@ UUGCAAGGG@LB@ \|\|:\|\|\|\|\|\|@LB@ AAUGUUCCC@LB@3'-UUU...UACUC GUGUC...GUG-5'@LB@ \| \|@LB@ 35 25@LB@@LB@@LB@Energy -8.77 kcal/mol@LB@Hybridization Energy -12.3281 kcal/mol@LB@Unfolding Energy - mRNA 0.874927 kcal/mol@LB@Unfolding Energy - sRNA 2.67841 kcal/mol@LB@@LB@Position - mRNA 243 -- 251@LB@Position - sRNA 26 -- 34@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 26 -- 32@LB@
157	0.009216	0.2062	b3361	fic	-9.77	0.153316	103 -- 112	5 -- 14	stationary phase-induced protein putative toxin	_____________102________113\n_____________\|__________\|\n5'-CGC...CGUAA__________AGUCG...AAC-3'\n______________UUUUCAGGCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________AAAAGUCCGG\n3'-UUU...UGACA__________CGUG-5'\n_____________\|__________\|\n_____________15_________4\n	106 -- 112	5 -- 11	-15.6889 kcal/mol	1.64573 kcal/mol	4.24834 kcal/mol	102 113@LB@ \| \|@LB@5'-CGC...CGUAA AGUCG...AAC-3'@LB@ UUUUCAGGCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ AAAAGUCCGG@LB@3'-UUU...UGACA CGUG-5'@LB@ \| \|@LB@ 15 4@LB@@LB@@LB@Energy -9.77 kcal/mol@LB@Hybridization Energy -15.6889 kcal/mol@LB@Unfolding Energy - mRNA 1.64573 kcal/mol@LB@Unfolding Energy - sRNA 4.24834 kcal/mol@LB@@LB@Position - mRNA 103 -- 112@LB@Position - sRNA 5 -- 14@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 5 -- 11@LB@
129	0.007194	0.1964	b3401	hslO	-8.25	0.287762	98 -- 107	1 -- 10	heat shock protein Hsp33	_____________97_________108\n_____________\|__________\|\n5'-GCC...UUAAC__U_______CCGGA...AGA-3'\n______________CA_GCCGCAC\n______________\|\|_\|\|\|\|\|\|\|\n______________GU_CGGCGUG\n3'-UUU...AAAAA__C_______-5'\n_____________\|_________\|\n_____________11________1\n	101 -- 107	1 -- 7	-14.7655 kcal/mol	1.13179 kcal/mol	5.44172 kcal/mol	97 108@LB@ \| \|@LB@5'-GCC...UUAAC U CCGGA...AGA-3'@LB@ CA GCCGCAC@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU CGGCGUG@LB@3'-UUU...AAAAA C -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -14.7655 kcal/mol@LB@Unfolding Energy - mRNA 1.13179 kcal/mol@LB@Unfolding Energy - sRNA 5.44172 kcal/mol@LB@@LB@Position - mRNA 98 -- 107@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 1 -- 7@LB@
141	0.008132	0.2031	b3412	bioH	-10.51	0.111302	230 -- 255	56 -- 74	pimeloyl-ACP methyl ester carboxylesterase	_____________229________________________256\n_____________\|__________________________\|\n5'-GGC...AAAGG________AUGUUC______U_____UGCAC...ACG-3'\n______________UCAGGGGA______AUCUUG_GCUGC\n______________:\|\|\|\|\|:\|______\|\|\|\|\|\|_\|\|\|\|\|\n______________GGUCCCUU______UAGAAC_CGACG\n3'-UUU...GUUGU__________________________CGGCA...GUG-5'\n_____________\|__________________________\|\n_____________75_________________________55\n	231 -- 237	67 -- 73	-25.2186 kcal/mol	6.56983 kcal/mol	8.13729 kcal/mol	229 256@LB@ \| \|@LB@5'-GGC...AAAGG AUGUUC U UGCAC...ACG-3'@LB@ UCAGGGGA AUCUUG GCUGC@LB@ :\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\|\|@LB@ GGUCCCUU UAGAAC CGACG@LB@3'-UUU...GUUGU CGGCA...GUG-5'@LB@ \| \|@LB@ 75 55@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -25.2186 kcal/mol@LB@Unfolding Energy - mRNA 6.56983 kcal/mol@LB@Unfolding Energy - sRNA 8.13729 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 56 -- 74@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 67 -- 73@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