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
13	0.0004028	0.1087	b1107	nagZ	-16.35	0.012500	184 -- 201	3 -- 21	beta N-acetyl-glucosaminidase	_____________183_________________202\n_____________\|___________________\|\n5'-AUU...AUAAA___AU______________UGGGU...CGC-3'\n______________ACA___AAGGAGAGCAGUG\n______________\|\|\|___\|\|\|:\|:\|\|\|\|\|\|\|\n______________UGU___UUCUUUUCGUCAC\n3'-UUU...ACCCC___AGU_____________CG-5'\n_____________\|___________________\|\n_____________22__________________2\n	195 -- 201	3 -- 9	-19.0842 kcal/mol	1.22154 kcal/mol	1.5107 kcal/mol	183 202@LB@ \| \|@LB@5'-AUU...AUAAA AU UGGGU...CGC-3'@LB@ ACA AAGGAGAGCAGUG@LB@ \|\|\| \|\|\|:\|:\|\|\|\|\|\|\|@LB@ UGU UUCUUUUCGUCAC@LB@3'-UUU...ACCCC AGU CG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -16.35 kcal/mol@LB@Hybridization Energy -19.0842 kcal/mol@LB@Unfolding Energy - mRNA 1.22154 kcal/mol@LB@Unfolding Energy - sRNA 1.5107 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 3 -- 9@LB@
122	0.008886	0.2491	b4366	bglJ	-14.76	0.031763	19 -- 32	15 -- 29	bgl operon transcriptional activator	_____________18______________33\n_____________\|_______________\|\n5'-CUG...GUAAA_______________CCAGA...GUA-3'\n______________GGAUGGGG_CAUCAA\n______________::\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UUUACCCC_GUAGUU\n3'-UUU...GGUGU________U______UCUUU...CCG-5'\n_____________\|_______________\|\n_____________30______________14\n	20 -- 26	22 -- 28	-19.2746 kcal/mol	3.84044 kcal/mol	0.677927 kcal/mol	18 33@LB@ \| \|@LB@5'-CUG...GUAAA CCAGA...GUA-3'@LB@ GGAUGGGG CAUCAA@LB@ ::\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUUACCCC GUAGUU@LB@3'-UUU...GGUGU U UCUUU...CCG-5'@LB@ \| \|@LB@ 30 14@LB@@LB@@LB@Energy -14.76 kcal/mol@LB@Hybridization Energy -19.2746 kcal/mol@LB@Unfolding Energy - mRNA 3.84044 kcal/mol@LB@Unfolding Energy - sRNA 0.677927 kcal/mol@LB@@LB@Position - mRNA 19 -- 32@LB@Position - sRNA 15 -- 29@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 22 -- 28@LB@
157	0.0114	0.2504	b3833	ubiE	-14.57	0.035245	198 -- 236	1 -- 30	bifunctional 2-octaprenyl-6-methoxy-1 4-benzoquinone methylase/ S-adenosylmethionine:2-DMK methyltransferase	_____________197_____________________________________237\n_____________\|_______________________________________\|\n5'-ACA...GCAUU_______U____AA____C______CGAC___CUU____UUUCA...CAU-3'\n______________GAGAUGG_GGAU__GUCA_AAGAAA____GCA___UGGU\n______________:\|:\|\|\|\|_\|\|\|:__:\|\|\|_\|\|\|\|\|\|____\|\|\|___\|\|\|:\n______________UUUUACC_CCUG__UAGU_UUCUUU____CGU___ACCG\n3'-UUU...AGGUG_________________________U______C______-5'\n_____________\|______________________________________\|\n_____________31_____________________________________1\n	198 -- 204	24 -- 30	-23.6374 kcal/mol	6.55293 kcal/mol	2.51911 kcal/mol	197 237@LB@ \| \|@LB@5'-ACA...GCAUU U AA C CGAC CUU UUUCA...CAU-3'@LB@ GAGAUGG GGAU GUCA AAGAAA GCA UGGU@LB@ :\|:\|\|\|\| \|\|\|: :\|\|\| \|\|\|\|\|\| \|\|\| \|\|\|:@LB@ UUUUACC CCUG UAGU UUCUUU CGU ACCG@LB@3'-UUU...AGGUG U C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -23.6374 kcal/mol@LB@Unfolding Energy - mRNA 6.55293 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 198 -- 236@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 24 -- 30@LB@
86	0.005461	0.2147	b0002	thrA	-11.41	0.159352	219 -- 235	1 -- 25	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________218_________________________236\n_____________\|___________________________\|\n5'-CCA...AGUUC__C__U_____________________AAAUG...UGG-3'\n______________GG_GG_ACAU__________CAGUGGC\n______________\|\|_\|\|_\|\|\|\|__________\|\|\|\|\|\|\|\n______________CC_CC_UGUA__________GUCACCG\n3'-UUU...UUUUA__________GUUUCUUUUC_______-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	229 -- 235	1 -- 7	-18.4664 kcal/mol	4.54068 kcal/mol	2.51748 kcal/mol	218 236@LB@ \| \|@LB@5'-CCA...AGUUC C U AAAUG...UGG-3'@LB@ GG GG ACAU CAGUGGC@LB@ \|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CC CC UGUA GUCACCG@LB@3'-UUU...UUUUA GUUUCUUUUC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -18.4664 kcal/mol@LB@Unfolding Energy - mRNA 4.54068 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 219 -- 235@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
177	0.01288	0.2504	b3455	livG	-10.61	0.218983	178 -- 198	5 -- 24	branched-chain amino acid ABC transporter ATPase	_____________177___________________199\n_____________\|_____________________\|\n5'-AUG...AAAAC__C___GCG____________GCAUG...UCG-3'\n______________GG_GCA___AAAGGAGAGCAG\n______________\|\|_:\|\|___\|\|\|\|:\|:\|\|\|\|\|\n______________CC_UGU___UUUCUUUUCGUC\n3'-UUU...UUUAC__C___AG_____________ACCG-5'\n_____________\|_____________________\|\n_____________25____________________4\n	192 -- 198	5 -- 11	-19.5574 kcal/mol	6.51739 kcal/mol	2.42705 kcal/mol	177 199@LB@ \| \|@LB@5'-AUG...AAAAC C GCG GCAUG...UCG-3'@LB@ GG GCA AAAGGAGAGCAG@LB@ \|\| :\|\| \|\|\|\|:\|:\|\|\|\|\|@LB@ CC UGU UUUCUUUUCGUC@LB@3'-UUU...UUUAC C AG ACCG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -19.5574 kcal/mol@LB@Unfolding Energy - mRNA 6.51739 kcal/mol@LB@Unfolding Energy - sRNA 2.42705 kcal/mol@LB@@LB@Position - mRNA 178 -- 198@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@LB@
48	0.002302	0.1648	b3460	livJ	-15.11	0.026091	183 -- 229	1 -- 30	branched-chain amino acid ABC transporter periplasmic binding protein	_____________182_____________________________________________230\n_____________\|_______________________________________________\|\n5'-AAU...CCAGA___________UC___GGAUGAACAUAA____U______UUAC____AGGAU...CAA-3'\n______________AGAAUGGGGAU__UCA____________AGGG_AAAGCG____UGGC\n______________\|:\|\|\|\|\|\|\|\|:__\|\|\|____________\|:\|:_\|\|\|\|\|:____\|\|\|\|\n______________UUUUACCCCUG__AGU____________UUCU_UUUCGU____ACCG\n3'-UUU...AGGUG___________U___________________________C_______-5'\n_____________\|______________________________________________\|\n_____________31_____________________________________________1\n	187 -- 193	20 -- 26	-27.0033 kcal/mol	9.37443 kcal/mol	2.51911 kcal/mol	182 230@LB@ \| \|@LB@5'-AAU...CCAGA UC GGAUGAACAUAA U UUAC AGGAU...CAA-3'@LB@ AGAAUGGGGAU UCA AGGG AAAGCG UGGC@LB@ \|:\|\|\|\|\|\|\|\|: \|\|\| \|:\|: \|\|\|\|\|: \|\|\|\|@LB@ UUUUACCCCUG AGU UUCU UUUCGU ACCG@LB@3'-UUU...AGGUG U C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -15.11 kcal/mol@LB@Hybridization Energy -27.0033 kcal/mol@LB@Unfolding Energy - mRNA 9.37443 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 183 -- 229@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 20 -- 26@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@
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@
34	0.001647	0.1648	b1218	chaC	-13.74	0.054411	171 -- 189	1 -- 17	cation transport regulator	_____________170_________________190\n_____________\|___________________\|\n5'-AUA...UGUCG________UAU________GGAAG...CGC-3'\n______________CAGGGAAG___GCAGUGGC\n______________\|\|::\|\|\|:___\|\|\|\|\|\|\|\|\n______________GUUUCUUU___CGUCACCG\n3'-UUU...CUGUA________U__________-5'\n_____________\|__________________\|\n_____________18_________________1\n	183 -- 189	1 -- 7	-23.3292 kcal/mol	8.15416 kcal/mol	1.43853 kcal/mol	170 190@LB@ \| \|@LB@5'-AUA...UGUCG UAU GGAAG...CGC-3'@LB@ CAGGGAAG GCAGUGGC@LB@ \|\|::\|\|\|: \|\|\|\|\|\|\|\|@LB@ GUUUCUUU CGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.74 kcal/mol@LB@Hybridization Energy -23.3292 kcal/mol@LB@Unfolding Energy - mRNA 8.15416 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 171 -- 189@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 1 -- 7@LB@
74	0.004177	0.1979	b2155	cirA	-15.75	0.017995	130 -- 157	1 -- 33	colicin IA outer membrane receptor and translocator; ferric iron-catecholate transporter	_____________129________________________________158\n_____________\|__________________________________\|\n5'-GGA...CCGUA_________________________U_____A__GAUAA...UGG-3'\n______________CGCAA___GGGGACGU_GAAGAAGA___GUG_GC\n______________\|:\|\|\|___\|\|\|\|\|\|:\|_:\|\|\|\|\|:\|___\|\|\|_\|\|\n______________GUGUU___CCCCUGUA_UUUCUUUU___CAC_CG\n3'-UUU...CCGAG_____UUA________G________CGU______-5'\n_____________\|_________________________________\|\n_____________34________________________________1\n	144 -- 150	9 -- 15	-28.6012 kcal/mol	9.77062 kcal/mol	3.07861 kcal/mol	129 158@LB@ \| \|@LB@5'-GGA...CCGUA U A GAUAA...UGG-3'@LB@ CGCAA GGGGACGU GAAGAAGA GUG GC@LB@ \|:\|\|\| \|\|\|\|\|\|:\| :\|\|\|\|\|:\| \|\|\| \|\|@LB@ GUGUU CCCCUGUA UUUCUUUU CAC CG@LB@3'-UUU...CCGAG UUA G CGU -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -15.75 kcal/mol@LB@Hybridization Energy -28.6012 kcal/mol@LB@Unfolding Energy - mRNA 9.77062 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 130 -- 157@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 9 -- 15@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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