Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
32	0.002002	0.2088	b0423	thiI	-12.47	0.034301	40 -- 74	41 -- 65	tRNA s(4)U8 sulfurtransferase	_____________39_____________________________________75\n_____________\|______________________________________\|\n5'-AUG...GUAAC___C____________AUAGCAAAUAACGC________AAGGU...UUU-3'\n______________GGA___UCAG_GGCAA______________GCAAUGGU\n______________\|\|\|___\|\|\|\|_\|\|\|\|\|______________\|\|\|\|\|\|\|:\n______________CCU___AGUC_CCGUU______________CGUUACCG\n3'-UUU...UACAA___UUU____A_____A_____________________GGUUG...UUG-5'\n_____________\|______________________________________\|\n_____________66_____________________________________40\n	68 -- 74	41 -- 47	-23.8518 kcal/mol	5.56921 kcal/mol	5.80973 kcal/mol	39 75@LB@ \| \|@LB@5'-AUG...GUAAC C AUAGCAAAUAACGC AAGGU...UUU-3'@LB@ GGA UCAG GGCAA GCAAUGGU@LB@ \|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\|:@LB@ CCU AGUC CCGUU CGUUACCG@LB@3'-UUU...UACAA UUU A A GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -12.47 kcal/mol@LB@Hybridization Energy -23.8518 kcal/mol@LB@Unfolding Energy - mRNA 5.56921 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 40 -- 74@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 41 -- 47@LB@
190	0.0237	0.4194	b0428	cyoE	-16.93	0.002220	1 -- 26	41 -- 65	protoheme IX farnesyltransferase	______________1__________________________27\n______________\|__________________________\|\n___________5'-____C____C________G________ACAGG...GCA-3'\n______________GGAA_AAUC__UGGCAAU_GCAGUGGU\n______________\|\|\|\|_\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|:\|\|\|:\n______________CCUU_UUAG__ACCGUUA_CGUUACCG\n3'-UUU...UACAA_________UC________________GGUUG...UUG-5'\n_____________\|___________________________\|\n_____________66__________________________40\n	20 -- 26	41 -- 47	-29.3415 kcal/mol	6.59984 kcal/mol	5.80973 kcal/mol	1 27@LB@ \| \|@LB@ 5'- C C G ACAGG...GCA-3'@LB@ GGAA AAUC UGGCAAU GCAGUGGU@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|\| \|\|\|:\|\|\|:@LB@ CCUU UUAG ACCGUUA CGUUACCG@LB@3'-UUU...UACAA UC GGUUG...UUG-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -16.93 kcal/mol@LB@Hybridization Energy -29.3415 kcal/mol@LB@Unfolding Energy - mRNA 6.59984 kcal/mol@LB@Unfolding Energy - sRNA 5.80973 kcal/mol@LB@@LB@Position - mRNA 1 -- 26@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 41 -- 47@LB@
180	0.02233	0.4143	b0435	bolA	-10.38	0.101210	35 -- 46	39 -- 51	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________34____________47\n_____________\|_____________\|\n5'-UGA...ACACU_____________GUGUU...CCG-3'\n______________GAUGCGA_GGCCU\n______________:\|\|\|\|:\|_\|\|\|\|:\n______________UUACGUU_CCGGG\n3'-UUU...CACCG_______A_____UUGUC...UUG-5'\n_____________\|_____________\|\n_____________52____________38\n	35 -- 41	45 -- 51	-16.689 kcal/mol	1.55914 kcal/mol	4.74571 kcal/mol	34 47@LB@ \| \|@LB@5'-UGA...ACACU GUGUU...CCG-3'@LB@ GAUGCGA GGCCU@LB@ :\|\|\|\|:\| \|\|\|\|:@LB@ UUACGUU CCGGG@LB@3'-UUU...CACCG A UUGUC...UUG-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.689 kcal/mol@LB@Unfolding Energy - mRNA 1.55914 kcal/mol@LB@Unfolding Energy - sRNA 4.74571 kcal/mol@LB@@LB@Position - mRNA 35 -- 46@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 45 -- 51@LB@
65	0.005052	0.2614	b0451	amtB	-9.90	0.127883	170 -- 220	11 -- 61	ammonium transporter	_____________169____________________________________________________221\n_____________\|______________________________________________________\|\n5'-CCA...GCUGU____UC_____CACA____CA__AA_______________AUA_C_________AACUG...CGU-3'\n______________AAUC__UGGCA____GCAA__GG__CGA___AAAAUGAAG___G_GACGAUAAA\n______________\|\|\|\|__\|\|\|\|\|____\|\|\|\|__\|\|__\|:\|___\|\|\|\|\|:\|\|:___\|_\|\|\|:\|\|\|\|\|\n______________UUAG__ACCGU____CGUU__CC__GUU___UUUUAUUUU___C_CUGUUAUUU\n3'-UUU...ACCUU____UC_____UA______A___GG___GUC_________AGA_A_________CCGUA...UUG-5'\n_____________\|______________________________________________________\|\n_____________62_____________________________________________________10\n	214 -- 220	11 -- 17	-30.4323 kcal/mol	9.41224 kcal/mol	11.1248 kcal/mol	169 221@LB@ \| \|@LB@5'-CCA...GCUGU UC CACA CA AA AUA C AACUG...CGU-3'@LB@ AAUC UGGCA GCAA GG CGA AAAAUGAAG G GACGAUAAA@LB@ \|\|\|\| \|\|\|\|\| \|\|\|\| \|\| \|:\| \|\|\|\|\|:\|\|: \| \|\|\|:\|\|\|\|\|@LB@ UUAG ACCGU CGUU CC GUU UUUUAUUUU C CUGUUAUUU@LB@3'-UUU...ACCUU UC UA A GG GUC AGA A CCGUA...UUG-5'@LB@ \| \|@LB@ 62 10@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -30.4323 kcal/mol@LB@Unfolding Energy - mRNA 9.41224 kcal/mol@LB@Unfolding Energy - sRNA 11.1248 kcal/mol@LB@@LB@Position - mRNA 170 -- 220@LB@Position - sRNA 11 -- 61@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 11 -- 17@LB@
56	0.003989	0.237	b0453	ybaY	-12.27	0.038324	59 -- 73	39 -- 55	outer membrane lipoprotein	_____________58________________74\n_____________\|_________________\|\n5'-AAG...UCCGA_________________GAAUU...CAA-3'\n______________UGG__GUGCAAUGGUCU\n______________\|\|\|__:\|\|\|\|\|\|\|\|:\|:\n______________ACC__UACGUUACCGGG\n3'-UUU...UAGUC___GU____________UUGUC...UUG-5'\n_____________\|_________________\|\n_____________56________________38\n	67 -- 73	39 -- 45	-20.8095 kcal/mol	3.77686 kcal/mol	4.76312 kcal/mol	58 74@LB@ \| \|@LB@5'-AAG...UCCGA GAAUU...CAA-3'@LB@ UGG GUGCAAUGGUCU@LB@ \|\|\| :\|\|\|\|\|\|\|\|:\|:@LB@ ACC UACGUUACCGGG@LB@3'-UUU...UAGUC GU UUGUC...UUG-5'@LB@ \| \|@LB@ 56 38@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -20.8095 kcal/mol@LB@Unfolding Energy - mRNA 3.77686 kcal/mol@LB@Unfolding Energy - sRNA 4.76312 kcal/mol@LB@@LB@Position - mRNA 59 -- 73@LB@Position - sRNA 39 -- 55@LB@Position Seed - mRNA 67 -- 73@LB@Position Seed - sRNA 39 -- 45@LB@
127	0.01373	0.3614	b0463	acrA	-13.78	0.016343	252 -- 289	8 -- 54	multidrug efflux system	_____________251________________________________________________290\n_____________\|__________________________________________________\|\n5'-GCC...UCUCA________UUA_____U________________________C__AC____CCAAC...GUG-3'\n______________GGCA__GC____GCCC_AACAGGA_________UGUGACGA_AA__AGGC\n______________\|\|\|\|__\|\|____\|\|\|\|_\|\|\|\|\|:\|_________\|\|\|\|\|\|:\|_\|\|__\|\|\|\|\n______________CCGU__CG____CGGG_UUGUCUU_________ACACUGUU_UU__UCCG\n3'-UUU...AGUCA____UA__UUAC____________UUAUUUUAG________A________UAUAUUG-5'\n_____________\|__________________________________________________\|\n_____________55_________________________________________________7\n	274 -- 280	15 -- 21	-34.7713 kcal/mol	8.97181 kcal/mol	12.019 kcal/mol	251 290@LB@ \| \|@LB@5'-GCC...UCUCA UUA U C AC CCAAC...GUG-3'@LB@ GGCA GC GCCC AACAGGA UGUGACGA AA AGGC@LB@ \|\|\|\| \|\| \|\|\|\| \|\|\|\|\|:\| \|\|\|\|\|\|:\| \|\| \|\|\|\|@LB@ CCGU CG CGGG UUGUCUU ACACUGUU UU UCCG@LB@3'-UUU...AGUCA UA UUAC UUAUUUUAG A UAUAUUG-5'@LB@ \| \|@LB@ 55 7@LB@@LB@@LB@Energy -13.78 kcal/mol@LB@Hybridization Energy -34.7713 kcal/mol@LB@Unfolding Energy - mRNA 8.97181 kcal/mol@LB@Unfolding Energy - sRNA 12.019 kcal/mol@LB@@LB@Position - mRNA 252 -- 289@LB@Position - sRNA 8 -- 54@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 15 -- 21@LB@
11	0.000438	0.1262	b0467	priC	-14.72	0.009297	1 -- 37	32 -- 65	primosomal replication protein N''	______________1____________________________________38\n______________\|____________________________________\|\n___________5'-______GAACG_____A___CCA___CG_________UAAAC...GUU-3'\n______________GGGGAA_____GGCAA_GCA___GGC__CCAGCAGGA\n______________\|\|::\|\|_____\|\|\|\|\|_\|\|\|___\|\|\|__\|\|\|:\|\|\|:\|\n______________CCUUUU_____CCGUU_CGU___CCG__GGUUGUCUU\n3'-UUU...UACAA______AGUCA_____A___UA_______________UUAUU...UUG-5'\n_____________\|_____________________________________\|\n_____________66____________________________________31\n	30 -- 36	33 -- 39	-34.0772 kcal/mol	8.3902 kcal/mol	10.9649 kcal/mol	1 38@LB@ \| \|@LB@ 5'- GAACG A CCA CG UAAAC...GUU-3'@LB@ GGGGAA GGCAA GCA GGC CCAGCAGGA@LB@ \|\|::\|\| \|\|\|\|\| \|\|\| \|\|\| \|\|\|:\|\|\|:\|@LB@ CCUUUU CCGUU CGU CCG GGUUGUCUU@LB@3'-UUU...UACAA AGUCA A UA UUAUU...UUG-5'@LB@ \| \|@LB@ 66 31@LB@@LB@@LB@Energy -14.72 kcal/mol@LB@Hybridization Energy -34.0772 kcal/mol@LB@Unfolding Energy - mRNA 8.3902 kcal/mol@LB@Unfolding Energy - sRNA 10.9649 kcal/mol@LB@@LB@Position - mRNA 1 -- 37@LB@Position - sRNA 32 -- 65@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 33 -- 39@LB@
122	0.01263	0.3462	b0537	intD	-10.49	0.096065	54 -- 80	48 -- 76	DLP12 prophage; putative phage integrase	_____________53____________________________81\n_____________\|_____________________________\|\n5'-GAG...AUUGG____________________A________ACGCA...AAG-3'\n______________UUUUGUAU_UUGGGGAG_CA_UGGCGAUG\n______________\|\|\|\|:\|\|\|_\|\|\|\|::\|:_\|\|_\|\|\|\|:\|\|\|\n______________AAAAUAUA_AACCUUUU_GU_ACCGUUAC\n3'-UUU...ACAGA________C________A__C________GUUAC...UUG-5'\n_____________\|_____________________________\|\n_____________77____________________________47\n	74 -- 80	48 -- 54	-25.3626 kcal/mol	9.83015 kcal/mol	5.0412 kcal/mol	53 81@LB@ \| \|@LB@5'-GAG...AUUGG A ACGCA...AAG-3'@LB@ UUUUGUAU UUGGGGAG CA UGGCGAUG@LB@ \|\|\|\|:\|\|\| \|\|\|\|::\|: \|\| \|\|\|\|:\|\|\|@LB@ AAAAUAUA AACCUUUU GU ACCGUUAC@LB@3'-UUU...ACAGA C A C GUUAC...UUG-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -25.3626 kcal/mol@LB@Unfolding Energy - mRNA 9.83015 kcal/mol@LB@Unfolding Energy - sRNA 5.0412 kcal/mol@LB@@LB@Position - mRNA 54 -- 80@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 48 -- 54@LB@
164	0.01912	0.392	b0585	fes	-11.27	0.064985	233 -- 253	39 -- 56	enterobactin/ferrienterobactin esterase	_____________232____________________254\n_____________\|______________________\|\n5'-CAU...AGCUG____________AACA______GGAAU...GGU-3'\n______________GUGGCAGU_CGA____UGGCCC\n______________\|\|\|\|\|\|:\|_\|:\|____\|\|\|\|\|\|\n______________CACCGUUA_GUU____ACCGGG\n3'-UUU...UUAGU________C_____________UUGUC...UUG-5'\n_____________\|______________________\|\n_____________57_____________________38\n	234 -- 240	49 -- 55	-24.6014 kcal/mol	8.56812 kcal/mol	4.76336 kcal/mol	232 254@LB@ \| \|@LB@5'-CAU...AGCUG AACA GGAAU...GGU-3'@LB@ GUGGCAGU CGA UGGCCC@LB@ \|\|\|\|\|\|:\| \|:\| \|\|\|\|\|\|@LB@ CACCGUUA GUU ACCGGG@LB@3'-UUU...UUAGU C UUGUC...UUG-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -24.6014 kcal/mol@LB@Unfolding Energy - mRNA 8.56812 kcal/mol@LB@Unfolding Energy - sRNA 4.76336 kcal/mol@LB@@LB@Position - mRNA 233 -- 253@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 49 -- 55@LB@
165	0.01953	0.3981	b0603	ybdO	-12.89	0.027143	166 -- 206	40 -- 73	putative DNA-binding transcriptional regulator	_____________165_________________________________________207\n_____________\|___________________________________________\|\n5'-UCA...GUGAA_____CA_______AAAAUAUAAC___A_______________AAUCU...CAC-3'\n______________UAUAU__UGGAAGA__________CGG__GUAGUGUA_UGGCC\n______________\|\|\|\|\|__\|\|\|\|\|:\|__________\|:\|__\|:\|:\|\|:\|_\|\|\|\|\|\n______________AUAUA__ACCUUUU__________GUC__CGUUACGU_ACCGG\n3'-UUU...GAAAA_____CA_______A____________AC________U_____GUUGU...UUG-5'\n_____________\|___________________________________________\|\n_____________74__________________________________________39\n	195 -- 201	46 -- 52	-24.6879 kcal/mol	4.92423 kcal/mol	6.86861 kcal/mol	165 207@LB@ \| \|@LB@5'-UCA...GUGAA CA AAAAUAUAAC A AAUCU...CAC-3'@LB@ UAUAU UGGAAGA CGG GUAGUGUA UGGCC@LB@ \|\|\|\|\| \|\|\|\|\|:\| \|:\| \|:\|:\|\|:\| \|\|\|\|\|@LB@ AUAUA ACCUUUU GUC CGUUACGU ACCGG@LB@3'-UUU...GAAAA CA A AC U GUUGU...UUG-5'@LB@ \| \|@LB@ 74 39@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -24.6879 kcal/mol@LB@Unfolding Energy - mRNA 4.92423 kcal/mol@LB@Unfolding Energy - sRNA 6.86861 kcal/mol@LB@@LB@Position - mRNA 166 -- 206@LB@Position - sRNA 40 -- 73@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 46 -- 52@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