Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
114	0.004808	0.1404	b2372	yfdV	-9.14	0.236047	240 -- 266	1 -- 35	putative transporter	_____________239____________________________________267\n_____________\|______________________________________\|\n5'-UUC...UUAUC___AU__U______________________________GGCAG...CUC-3'\n______________GUA__CA_GCU_GU______UGGGUUAU____UUUAGC\n______________\|\|\|__\|\|_\|\|\|_\|:______\|\|\|\|\|\|\|\|____\|\|:\|\|\|\n______________CAU__GU_CGA_CG______ACCCAAUA____AAGUCG\n3'-UUU...AGGAC___________U__UAAAAU________CAAA______-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	254 -- 260	11 -- 17	-17.7969 kcal/mol	7.16419 kcal/mol	1.49508 kcal/mol	239 267@LB@ \| \|@LB@5'-UUC...UUAUC AU U GGCAG...CUC-3'@LB@ GUA CA GCU GU UGGGUUAU UUUAGC@LB@ \|\|\| \|\| \|\|\| \|: \|\|\|\|\|\|\|\| \|\|:\|\|\|@LB@ CAU GU CGA CG ACCCAAUA AAGUCG@LB@3'-UUU...AGGAC U UAAAAU CAAA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -17.7969 kcal/mol@LB@Unfolding Energy - mRNA 7.16419 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 240 -- 266@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 11 -- 17@LB@
36	0.0006761	0.06313	b0759	galE	-8.98	0.250354	205 -- 236	22 -- 48	UDP-galactose-4-epimerase	_____________204_______________________________237\n_____________\|_________________________________\|\n5'-GCA...UAUGA___UUC_____A__GG____A____________GGAAG...UCU-3'\n______________GAG___UGGUU_CC__UGGU_GCGGUUA_CAUU\n______________\|\|\|___\|\|\|\|\|_\|\|__\|\|\|\|_:\|:\|:\|\|_\|\|\|\|\n______________CUC___ACCAA_GG__ACCA_UGUCGAU_GUAA\n3'-UUU...GAUUC___C________________________C____AAUAC...UCG-5'\n_____________\|_________________________________\|\n_____________49________________________________21\n	226 -- 232	27 -- 33	-23.3933 kcal/mol	9.85191 kcal/mol	4.55969 kcal/mol	204 237@LB@ \| \|@LB@5'-GCA...UAUGA UUC A GG A GGAAG...UCU-3'@LB@ GAG UGGUU CC UGGU GCGGUUA CAUU@LB@ \|\|\| \|\|\|\|\| \|\| \|\|\|\| :\|:\|:\|\| \|\|\|\|@LB@ CUC ACCAA GG ACCA UGUCGAU GUAA@LB@3'-UUU...GAUUC C C AAUAC...UCG-5'@LB@ \| \|@LB@ 49 21@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -23.3933 kcal/mol@LB@Unfolding Energy - mRNA 9.85191 kcal/mol@LB@Unfolding Energy - sRNA 4.55969 kcal/mol@LB@@LB@Position - mRNA 205 -- 236@LB@Position - sRNA 22 -- 48@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 27 -- 33@LB@
186	0.01069	0.1919	b1614	ydgA	-8.85	0.262719	182 -- 191	16 -- 25	DUF945 family protein	_____________181________192\n_____________\|__________\|\n5'-ACA...GAUUU__________AUAAU...UCG-3'\n______________CAUUUUAUGG\n______________\|\|\|\|\|\|\|\|\|\|\n______________GUAAAAUACC\n3'-UUU...CGAUC__________CAAUA...UCG-5'\n_____________\|__________\|\n_____________26_________15\n	185 -- 191	16 -- 22	-11.3536 kcal/mol	2.1555 kcal/mol	0.346409 kcal/mol	181 192@LB@ \| \|@LB@5'-ACA...GAUUU AUAAU...UCG-3'@LB@ CAUUUUAUGG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GUAAAAUACC@LB@3'-UUU...CGAUC CAAUA...UCG-5'@LB@ \| \|@LB@ 26 15@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -11.3536 kcal/mol@LB@Unfolding Energy - mRNA 2.1555 kcal/mol@LB@Unfolding Energy - sRNA 0.346409 kcal/mol@LB@@LB@Position - mRNA 182 -- 191@LB@Position - sRNA 16 -- 25@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 16 -- 22@LB@
172	0.009254	0.1803	b1676	pykF	-8.82	0.265733	268 -- 283	23 -- 40	pyruvate kinase I	_____________267________________284\n_____________\|__________________\|\n5'-GGA...UAAAA_G________________GAACG...UGA-3'\n______________U_CUGG_AC_GCUGGCAU\n______________\|_\|\|\|\|_\|\|_\|\|\|:\|\|\|\|\n______________A_GACC_UG_CGAUCGUA\n3'-UUU...CACCA_G____A__U________AAAUA...UCG-5'\n_____________\|__________________\|\n_____________41_________________22\n	277 -- 283	23 -- 29	-20.12 kcal/mol	6.74388 kcal/mol	4.55554 kcal/mol	267 284@LB@ \| \|@LB@5'-GGA...UAAAA G GAACG...UGA-3'@LB@ U CUGG AC GCUGGCAU@LB@ \| \|\|\|\| \|\| \|\|\|:\|\|\|\|@LB@ A GACC UG CGAUCGUA@LB@3'-UUU...CACCA G A U AAAUA...UCG-5'@LB@ \| \|@LB@ 41 22@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -20.12 kcal/mol@LB@Unfolding Energy - mRNA 6.74388 kcal/mol@LB@Unfolding Energy - sRNA 4.55554 kcal/mol@LB@@LB@Position - mRNA 268 -- 283@LB@Position - sRNA 23 -- 40@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 23 -- 29@LB@
146	0.006865	0.158	b2701	mltB	-8.70	0.277719	77 -- 106	9 -- 36	membrane-bound lytic murein transglycosylase B	_____________76______________________________107\n_____________\|_______________________________\|\n5'-AGA...UAAAA________G__G_GAAUGAGU__A_______AAAGU...GAA-3'\n______________GG_AUAGC_AG_G________UG_GUUAUGU\n______________\|\|_\|:\|\|\|_\|\|_:________\|\|_\|\|\|\|\|\|\|\n______________CC_UGUCG_UC_U________AC_CAAUACA\n3'-UUU...AAGGA__A_____A__G_AAAAU_____C_______AAAAGUCG-5'\n_____________\|_______________________________\|\n_____________37______________________________8\n	100 -- 106	9 -- 15	-15.8871 kcal/mol	5.69864 kcal/mol	1.48926 kcal/mol	76 107@LB@ \| \|@LB@5'-AGA...UAAAA G G GAAUGAGU A AAAGU...GAA-3'@LB@ GG AUAGC AG G UG GUUAUGU@LB@ \|\| \|:\|\|\| \|\| : \|\| \|\|\|\|\|\|\|@LB@ CC UGUCG UC U AC CAAUACA@LB@3'-UUU...AAGGA A A G AAAAU C AAAAGUCG-5'@LB@ \| \|@LB@ 37 8@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -15.8871 kcal/mol@LB@Unfolding Energy - mRNA 5.69864 kcal/mol@LB@Unfolding Energy - sRNA 1.48926 kcal/mol@LB@@LB@Position - mRNA 77 -- 106@LB@Position - sRNA 9 -- 36@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 9 -- 15@LB@
60	0.001479	0.08283	b1886	tar	-8.65	0.283085	258 -- 290	4 -- 38	methyl-accepting chemotaxis protein II	_____________257__________________________________291\n_____________\|____________________________________\|\n5'-UGC...UCGCA___U______________CC___CAGUC________UCUUC...UUC-3'\n______________CUG_UACAGCU__UAUUU___GG_____UGUUUUUU\n______________\|\|\|_\|\|\|\|\|\|\|__:\|\|\|\|___\|\|_____\|\|\|\|\|\|\|:\n______________GAC_AUGUCGA__GUAAA___CC_____ACAAAAAG\n3'-UUU...CCAAG___C_______UC_____AUA__CAAU_________UCG-5'\n_____________\|____________________________________\|\n_____________39___________________________________3\n	284 -- 290	4 -- 10	-19.1357 kcal/mol	5.94997 kcal/mol	4.53981 kcal/mol	257 291@LB@ \| \|@LB@5'-UGC...UCGCA U CC CAGUC UCUUC...UUC-3'@LB@ CUG UACAGCU UAUUU GG UGUUUUUU@LB@ \|\|\| \|\|\|\|\|\|\| :\|\|\|\| \|\| \|\|\|\|\|\|\|:@LB@ GAC AUGUCGA GUAAA CC ACAAAAAG@LB@3'-UUU...CCAAG C UC AUA CAAU UCG-5'@LB@ \| \|@LB@ 39 3@LB@@LB@@LB@Energy -8.65 kcal/mol@LB@Hybridization Energy -19.1357 kcal/mol@LB@Unfolding Energy - mRNA 5.94997 kcal/mol@LB@Unfolding Energy - sRNA 4.53981 kcal/mol@LB@@LB@Position - mRNA 258 -- 290@LB@Position - sRNA 4 -- 38@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 4 -- 10@LB@
189	0.01085	0.1919	b3606	trmL	-8.64	0.283903	120 -- 126	63 -- 69	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent	_____________119_____127\n_____________\|_______\|\n5'-UAG...CCUCC_______GGGCC...AAC-3'\n______________GGGGAGA\n______________:\|\|\|\|\|\|\n______________UCCCUCU\n3'-UUU...CACAU_______AAUGU...UCG-5'\n_____________\|_______\|\n_____________70______62\n	120 -- 126	63 -- 69	-10.8913 kcal/mol	1.31422 kcal/mol	0.939295 kcal/mol	119 127@LB@ \| \|@LB@5'-UAG...CCUCC GGGCC...AAC-3'@LB@ GGGGAGA@LB@ :\|\|\|\|\|\|@LB@ UCCCUCU@LB@3'-UUU...CACAU AAUGU...UCG-5'@LB@ \| \|@LB@ 70 62@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -10.8913 kcal/mol@LB@Unfolding Energy - mRNA 1.31422 kcal/mol@LB@Unfolding Energy - sRNA 0.939295 kcal/mol@LB@@LB@Position - mRNA 120 -- 126@LB@Position - sRNA 63 -- 69@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 63 -- 69@LB@
41	0.0008276	0.06626	b1218	chaC	-8.54	0.293650	119 -- 139	24 -- 45	cation transport regulator	_____________118____________________140\n_____________\|______________________\|\n5'-AUA...CGUUA________AAAAUG________AAAAU...CGC-3'\n______________GUGGUUUC______AGC_AGUA\n______________\|\|\|\|\|\|:\|______\|\|\|_\|\|:\|\n______________CACCAAGG______UCG_UCGU\n3'-UUU...UCCUC________ACCAUG___A____AAAAU...UCG-5'\n_____________\|______________________\|\n_____________46_____________________23\n	120 -- 126	38 -- 44	-17.6586 kcal/mol	4.55792 kcal/mol	4.55794 kcal/mol	118 140@LB@ \| \|@LB@5'-AUA...CGUUA AAAAUG AAAAU...CGC-3'@LB@ GUGGUUUC AGC AGUA@LB@ \|\|\|\|\|\|:\| \|\|\| \|\|:\|@LB@ CACCAAGG UCG UCGU@LB@3'-UUU...UCCUC ACCAUG A AAAAU...UCG-5'@LB@ \| \|@LB@ 46 23@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -17.6586 kcal/mol@LB@Unfolding Energy - mRNA 4.55792 kcal/mol@LB@Unfolding Energy - sRNA 4.55794 kcal/mol@LB@@LB@Position - mRNA 119 -- 139@LB@Position - sRNA 24 -- 45@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 38 -- 44@LB@
132	0.005751	0.146	b2294	yfbU	-8.39	0.309344	3 -- 25	24 -- 50	UPF0304 family protein	_____________2______________________________26\n_____________\|______________________________\|\n_________5'-GC____________________GGU_______CCCGU...AAA-3'\n______________AGGAG______UCUGG_ACA___GUUGGCA\n______________\|\|\|\|\|______:\|\|\|\|_\|\|\|___\|:\|:\|\|\|\n______________UCCUC______GGACC_UGU___CGAUCGU\n3'-UUU...CCGAU_____CACCAA_____A_____________AAAAU...UCG-5'\n_____________\|______________________________\|\n_____________51_____________________________23\n	19 -- 25	24 -- 30	-20.5947 kcal/mol	7.58762 kcal/mol	4.6134 kcal/mol	2 26@LB@ \| \|@LB@ 5'-GC GGU CCCGU...AAA-3'@LB@ AGGAG UCUGG ACA GUUGGCA@LB@ \|\|\|\|\| :\|\|\|\| \|\|\| \|:\|:\|\|\|@LB@ UCCUC GGACC UGU CGAUCGU@LB@3'-UUU...CCGAU CACCAA A AAAAU...UCG-5'@LB@ \| \|@LB@ 51 23@LB@@LB@@LB@Energy -8.39 kcal/mol@LB@Hybridization Energy -20.5947 kcal/mol@LB@Unfolding Energy - mRNA 7.58762 kcal/mol@LB@Unfolding Energy - sRNA 4.6134 kcal/mol@LB@@LB@Position - mRNA 3 -- 25@LB@Position - sRNA 24 -- 50@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 24 -- 30@LB@
121	0.005123	0.1413	b1735	chbR	-8.25	0.324466	38 -- 46	30 -- 38	repressor of chb operon for N N'-diacetylchitobiose utilization	_____________37________47\n_____________\|_________\|\n5'-GAU...CGCAU_________ACGAA...CUG-3'\n______________CUGGUACAG\n______________\|\|\|\|\|\|\|\|\|\n______________GACCAUGUC\n3'-UUU...CCAAG_________GAUCG...UCG-5'\n_____________\|_________\|\n_____________39________29\n	40 -- 46	30 -- 36	-15.5432 kcal/mol	3.07825 kcal/mol	4.2107 kcal/mol	37 47@LB@ \| \|@LB@5'-GAU...CGCAU ACGAA...CUG-3'@LB@ CUGGUACAG@LB@ \|\|\|\|\|\|\|\|\|@LB@ GACCAUGUC@LB@3'-UUU...CCAAG GAUCG...UCG-5'@LB@ \| \|@LB@ 39 29@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -15.5432 kcal/mol@LB@Unfolding Energy - mRNA 3.07825 kcal/mol@LB@Unfolding Energy - sRNA 4.2107 kcal/mol@LB@@LB@Position - mRNA 38 -- 46@LB@Position - sRNA 30 -- 38@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 30 -- 36@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