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
158	0.01161	0.2504	b3907	rhaT	-15.90	0.016445	218 -- 234	1 -- 28	L-rhamnose:proton symporter	_____________217__________________________235\n_____________\|____________________________\|\n5'-AUG...AUUAC____________U_______________AUUUG...CAU-3'\n______________GAUGGGGAUAUU____________UGGC\n______________:\|\|\|\|\|\|\|:\|\|:____________\|\|\|\|\n______________UUACCCCUGUAG____________ACCG\n3'-UUU...GUGUU____________UUUCUUUUCGUC____-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	223 -- 229	17 -- 23	-20.3321 kcal/mol	1.91011 kcal/mol	2.519 kcal/mol	217 235@LB@ \| \|@LB@5'-AUG...AUUAC U AUUUG...CAU-3'@LB@ GAUGGGGAUAUU UGGC@LB@ :\|\|\|\|\|\|\|:\|\|: \|\|\|\|@LB@ UUACCCCUGUAG ACCG@LB@3'-UUU...GUGUU UUUCUUUUCGUC -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -20.3321 kcal/mol@LB@Unfolding Energy - mRNA 1.91011 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 218 -- 234@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 17 -- 23@LB@
159	0.01174	0.2504	b3886	yihY	-12.46	0.100688	17 -- 39	6 -- 26	BrkB family putative transporter inner membrane protein	_____________16______________________40\n_____________\|_______________________\|\n5'-UAU...AGAUC________CG____CCU______CGAAU...CAA-3'\n______________UGGGGAUG__CAAA___GAAGCA\n______________\|\|\|\|\|\|::__\|\|\|\|___:\|\|\|\|\|\n______________ACCCCUGU__GUUU___UUUCGU\n3'-UUU...GUUUU________A_____CU_______CACCG-5'\n_____________\|_______________________\|\n_____________27______________________5\n	18 -- 24	19 -- 25	-18.1196 kcal/mol	4.95346 kcal/mol	0.706421 kcal/mol	16 40@LB@ \| \|@LB@5'-UAU...AGAUC CG CCU CGAAU...CAA-3'@LB@ UGGGGAUG CAAA GAAGCA@LB@ \|\|\|\|\|\|:: \|\|\|\| :\|\|\|\|\|@LB@ ACCCCUGU GUUU UUUCGU@LB@3'-UUU...GUUUU A CU CACCG-5'@LB@ \| \|@LB@ 27 5@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -18.1196 kcal/mol@LB@Unfolding Energy - mRNA 4.95346 kcal/mol@LB@Unfolding Energy - sRNA 0.706421 kcal/mol@LB@@LB@Position - mRNA 17 -- 39@LB@Position - sRNA 6 -- 26@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 19 -- 25@LB@
160	0.0118	0.2504	b0078	ilvH	-13.58	0.059018	151 -- 175	1 -- 25	acetolactate synthase 3 small subunit valine-sensitive	_____________150_______________________176\n_____________\|_________________________\|\n5'-GCC...UUCGC_______GAAU___UGAAAU_____UAAGC...UGA-3'\n______________GGGGGCG____GGA______GUGGU\n______________\|\|\|\|:\|:____:\|\|______\|\|\|\|:\n______________CCCCUGU____UCU______CACCG\n3'-UUU...UUUUA_______AGUU___UUUCGU_____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	151 -- 157	19 -- 25	-21.9405 kcal/mol	5.84786 kcal/mol	2.51748 kcal/mol	150 176@LB@ \| \|@LB@5'-GCC...UUCGC GAAU UGAAAU UAAGC...UGA-3'@LB@ GGGGGCG GGA GUGGU@LB@ \|\|\|\|:\|: :\|\| \|\|\|\|:@LB@ CCCCUGU UCU CACCG@LB@3'-UUU...UUUUA AGUU UUUCGU -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -21.9405 kcal/mol@LB@Unfolding Energy - mRNA 5.84786 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 151 -- 175@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 19 -- 25@LB@
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@
162	0.012	0.2504	b2079	baeR	-15.58	0.019969	182 -- 201	6 -- 24	response regulator in two-component regulatory system with BaeS	_____________181__________________202\n_____________\|____________________\|\n5'-CAG...GGAAC_____UUA____________UGACC...CGA-3'\n______________GGGAU___CAGAGAGAAGUA\n______________\|\|\|\|:___\|\|:\|\|\|:\|\|\|:\|\n______________CCCUG___GUUUCUUUUCGU\n3'-UUU...UUUAC_____UA_____________CACCG-5'\n_____________\|____________________\|\n_____________25___________________5\n	195 -- 201	6 -- 12	-20.602 kcal/mol	4.32458 kcal/mol	0.702143 kcal/mol	181 202@LB@ \| \|@LB@5'-CAG...GGAAC UUA UGACC...CGA-3'@LB@ GGGAU CAGAGAGAAGUA@LB@ \|\|\|\|: \|\|:\|\|\|:\|\|\|:\|@LB@ CCCUG GUUUCUUUUCGU@LB@3'-UUU...UUUAC UA CACCG-5'@LB@ \| \|@LB@ 25 5@LB@@LB@@LB@Energy -15.58 kcal/mol@LB@Hybridization Energy -20.602 kcal/mol@LB@Unfolding Energy - mRNA 4.32458 kcal/mol@LB@Unfolding Energy - sRNA 0.702143 kcal/mol@LB@@LB@Position - mRNA 182 -- 201@LB@Position - sRNA 6 -- 24@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 6 -- 12@LB@
163	0.01202	0.2504	b1482	osmC	-10.53	0.225653	203 -- 226	1 -- 22	lipoyl-dependent Cys-based peroxidase hydroperoxide resistance; salt-shock inducible membrane protein; peroxiredoxin	_____________202_______________________227\n_____________\|_________________________\|\n5'-UAG...ACAAU___A___CAU_________CA____ACACU...CGU-3'\n______________GAC_AUC___AAGAAAGGU___GGC\n______________\|\|\|_\|\|\|___\|\|\|\|\|\|:\|:___\|\|\|\n______________CUG_UAG___UUCUUUUCG___CCG\n3'-UUU...UACCC_______U___________UCA___-5'\n_____________\|________________________\|\n_____________23_______________________1\n	215 -- 221	7 -- 13	-17.1921 kcal/mol	5.11752 kcal/mol	1.54023 kcal/mol	202 227@LB@ \| \|@LB@5'-UAG...ACAAU A CAU CA ACACU...CGU-3'@LB@ GAC AUC AAGAAAGGU GGC@LB@ \|\|\| \|\|\| \|\|\|\|\|\|:\|: \|\|\|@LB@ CUG UAG UUCUUUUCG CCG@LB@3'-UUU...UACCC U UCA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -17.1921 kcal/mol@LB@Unfolding Energy - mRNA 5.11752 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 7 -- 13@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@
165	0.01211	0.2504	b3642	pyrE	-11.74	0.138291	22 -- 41	7 -- 25	orotate phosphoribosyltransferase	_____________21___________________42\n_____________\|____________________\|\n5'-CGG...GUGCA_______GCA_____C____CGUUC...AUU-3'\n______________GGGGACG___GAAGG_GAGC\n______________\|\|\|\|\|\|:___:\|\|\|:_:\|\|\|\n______________CCCCUGU___UUUCU_UUCG\n3'-UUU...UUUUA_______AG______U____UCACCG-5'\n_____________\|____________________\|\n_____________26___________________6\n	22 -- 28	19 -- 25	-22.5653 kcal/mol	10.1153 kcal/mol	0.70626 kcal/mol	21 42@LB@ \| \|@LB@5'-CGG...GUGCA GCA C CGUUC...AUU-3'@LB@ GGGGACG GAAGG GAGC@LB@ \|\|\|\|\|\|: :\|\|\|: :\|\|\|@LB@ CCCCUGU UUUCU UUCG@LB@3'-UUU...UUUUA AG U UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -22.5653 kcal/mol@LB@Unfolding Energy - mRNA 10.1153 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 22 -- 41@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 19 -- 25@LB@
166	0.01216	0.2504	b4485	ytfR	-12.60	0.094393	18 -- 41	9 -- 34	putative sugar ABC transporter ATPase	_____________17_________________________42\n_____________\|__________________________\|\n5'-CCU...UGAUA________GAA_______________AGAAA...GCC-3'\n______________CCGCAAAA____GA_AUUAGAGAAGA\n______________\|\|:\|\|\|\|\|____\|\|_\|\|:\|:\|\|\|\|:\|\n______________GGUGUUUU____CU_UAGUUUCUUUU\n3'-UUU...CCCGA________ACCC__G___________CGUCACCG-5'\n_____________\|__________________________\|\n_____________35_________________________8\n	35 -- 41	9 -- 15	-17.8797 kcal/mol	1.35017 kcal/mol	3.92941 kcal/mol	17 42@LB@ \| \|@LB@5'-CCU...UGAUA GAA AGAAA...GCC-3'@LB@ CCGCAAAA GA AUUAGAGAAGA@LB@ \|\|:\|\|\|\|\| \|\| \|\|:\|:\|\|\|\|:\|@LB@ GGUGUUUU CU UAGUUUCUUUU@LB@3'-UUU...CCCGA ACCC G CGUCACCG-5'@LB@ \| \|@LB@ 35 8@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -17.8797 kcal/mol@LB@Unfolding Energy - mRNA 1.35017 kcal/mol@LB@Unfolding Energy - sRNA 3.92941 kcal/mol@LB@@LB@Position - mRNA 18 -- 41@LB@Position - sRNA 9 -- 34@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 9 -- 15@LB@
168	0.01219	0.2504	b1830	prc	-10.01	0.273454	1 -- 12	6 -- 17	carboxy-terminal protease for penicillin-binding protein 3	______________1___________13\n______________\|___________\|\n___________5'-_______C____CACCC...CGG-3'\n______________CGAAGAA_AGCA\n______________\|:\|\|\|\|\|_\|\|\|\|\n______________GUUUCUU_UCGU\n3'-UUU...CUGUA_______U____CACCG-5'\n_____________\|____________\|\n_____________18___________5\n	1 -- 7	11 -- 17	-11.3077 kcal/mol	0.751361 kcal/mol	0.542636 kcal/mol	1 13@LB@ \| \|@LB@ 5'- C CACCC...CGG-3'@LB@ CGAAGAA AGCA@LB@ \|:\|\|\|\|\| \|\|\|\|@LB@ GUUUCUU UCGU@LB@3'-UUU...CUGUA U CACCG-5'@LB@ \| \|@LB@ 18 5@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -11.3077 kcal/mol@LB@Unfolding Energy - mRNA 0.751361 kcal/mol@LB@Unfolding Energy - sRNA 0.542636 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 6 -- 17@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 11 -- 17@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)

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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

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