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
183	0.01318	0.2504	b4483	tatD	-12.95	0.080004	100 -- 117	8 -- 25	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase	_____________99__________________118\n_____________\|___________________\|\n5'-CUG...GUAAA___C__A____________GAAAA...UCA-3'\n______________GGG_GA_AUC_GGGAAGAG\n______________\|\|\|_\|\|_\|\|\|_::\|\|\|:\|\|\n______________CCC_CU_UAG_UUCUUUUC\n3'-UUU...UUUUA______G___U________GUCACCG-5'\n_____________\|___________________\|\n_____________26__________________7\n	111 -- 117	8 -- 14	-16.1661 kcal/mol	2.51597 kcal/mol	0.697717 kcal/mol	99 118@LB@ \| \|@LB@5'-CUG...GUAAA C A GAAAA...UCA-3'@LB@ GGG GA AUC GGGAAGAG@LB@ \|\|\| \|\| \|\|\| ::\|\|\|:\|\|@LB@ CCC CU UAG UUCUUUUC@LB@3'-UUU...UUUUA G U GUCACCG-5'@LB@ \| \|@LB@ 26 7@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -16.1661 kcal/mol@LB@Unfolding Energy - mRNA 2.51597 kcal/mol@LB@Unfolding Energy - sRNA 0.697717 kcal/mol@LB@@LB@Position - mRNA 100 -- 117@LB@Position - sRNA 8 -- 25@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 8 -- 14@LB@
147	0.01091	0.2504	b2720	hycF	-14.84	0.030299	116 -- 133	1 -- 16	formate hydrogenlyase complex iron-sulfur protein	_____________115________________134\n_____________\|__________________\|\n5'-CGA...CGUAA___________AA_____GCCGU...CAG-3'\n______________GAAGAAGAGCA__GUGGU\n______________:\|\|\|\|\|:\|\|\|\|__\|\|\|\|:\n______________UUUCUUUUCGU__CACCG\n3'-UUU...UGUAG__________________-5'\n_____________\|_________________\|\n_____________17________________1\n	120 -- 126	6 -- 12	-19.8629 kcal/mol	3.67538 kcal/mol	1.34555 kcal/mol	115 134@LB@ \| \|@LB@5'-CGA...CGUAA AA GCCGU...CAG-3'@LB@ GAAGAAGAGCA GUGGU@LB@ :\|\|\|\|\|:\|\|\|\| \|\|\|\|:@LB@ UUUCUUUUCGU CACCG@LB@3'-UUU...UGUAG -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -19.8629 kcal/mol@LB@Unfolding Energy - mRNA 3.67538 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 116 -- 133@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 6 -- 12@LB@
182	0.01317	0.2504	b2101	yegW	-15.40	0.022099	126 -- 162	3 -- 28	putative DNA-binding transcriptional regulator	_____________125______________________________________163\n_____________\|________________________________________\|\n5'-CGG...UCGUU_________________AACGCCUUAAAUAA_________AUAUA...AAA-3'\n______________GAUGGG___AUUAAAGA______________GAAGCAGUG\n______________:\|\|\|\|\|___\|\|:\|\|\|\|\|______________:\|\|\|\|\|\|\|\|\n______________UUACCC___UAGUUUCU______________UUUCGUCAC\n3'-UUU...GUGUU______CUG_______________________________CG-5'\n_____________\|________________________________________\|\n_____________29_______________________________________2\n	156 -- 162	3 -- 9	-24.3736 kcal/mol	6.45453 kcal/mol	2.51813 kcal/mol	125 163@LB@ \| \|@LB@5'-CGG...UCGUU AACGCCUUAAAUAA AUAUA...AAA-3'@LB@ GAUGGG AUUAAAGA GAAGCAGUG@LB@ :\|\|\|\|\| \|\|:\|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ UUACCC UAGUUUCU UUUCGUCAC@LB@3'-UUU...GUGUU CUG CG-5'@LB@ \| \|@LB@ 29 2@LB@@LB@@LB@Energy -15.40 kcal/mol@LB@Hybridization Energy -24.3736 kcal/mol@LB@Unfolding Energy - mRNA 6.45453 kcal/mol@LB@Unfolding Energy - sRNA 2.51813 kcal/mol@LB@@LB@Position - mRNA 126 -- 162@LB@Position - sRNA 3 -- 28@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 3 -- 9@LB@
148	0.01095	0.2504	b0082	rsmH	-17.59	0.005541	130 -- 156	1 -- 25	16S rRNA m(4)C1402 methyltransferase SAM-dependent	_____________129_________________________157\n_____________\|___________________________\|\n5'-UGG...GUCAA__AA________C_C________U___UACCG...GUC-3'\n______________GG__GAUAUCGA_G_AGAGCAGU_GGC\n______________\|\|__\|\|:\|\|\|:\|_\|_\|:\|\|\|\|\|\|_\|\|\|\n______________CC__CUGUAGUU_C_UUUCGUCA_CCG\n3'-UUU...UUUUA__C_________U_U____________-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	146 -- 152	4 -- 10	-26.6505 kcal/mol	6.5392 kcal/mol	2.51748 kcal/mol	129 157@LB@ \| \|@LB@5'-UGG...GUCAA AA C C U UACCG...GUC-3'@LB@ GG GAUAUCGA G AGAGCAGU GGC@LB@ \|\| \|\|:\|\|\|:\| \| \|:\|\|\|\|\|\| \|\|\|@LB@ CC CUGUAGUU C UUUCGUCA CCG@LB@3'-UUU...UUUUA C U U -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -17.59 kcal/mol@LB@Hybridization Energy -26.6505 kcal/mol@LB@Unfolding Energy - mRNA 6.5392 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 130 -- 156@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 4 -- 10@LB@
151	0.01116	0.2504	b0903	pflB	-10.70	0.211701	140 -- 166	4 -- 34	formate C-acetyltransferase 1 anaerobic; pyruvate formate-lyase 1	_____________139_____________________________167\n_____________\|_______________________________\|\n5'-CAC...GACCA____U______U__________UAC______AAAUA...ACU-3'\n______________CCAU__AAUGG___UGUCGAAG____GCAGU\n______________\|\|\|:__\|\|\|\|\|___::\|\|:\|\|\|____\|\|\|\|\|\n______________GGUG__UUACC___GUAGUUUC____CGUCA\n3'-UUU...CCCGA____UU_____CCU________UUUU_____CCG-5'\n_____________\|_______________________________\|\n_____________35______________________________3\n	152 -- 158	13 -- 19	-21.5315 kcal/mol	6.56187 kcal/mol	4.26884 kcal/mol	139 167@LB@ \| \|@LB@5'-CAC...GACCA U U UAC AAAUA...ACU-3'@LB@ CCAU AAUGG UGUCGAAG GCAGU@LB@ \|\|\|: \|\|\|\|\| ::\|\|:\|\|\| \|\|\|\|\|@LB@ GGUG UUACC GUAGUUUC CGUCA@LB@3'-UUU...CCCGA UU CCU UUUU CCG-5'@LB@ \| \|@LB@ 35 3@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -21.5315 kcal/mol@LB@Unfolding Energy - mRNA 6.56187 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 140 -- 166@LB@Position - sRNA 4 -- 34@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 13 -- 19@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@
153	0.01124	0.2504	b0414	ribD	-14.78	0.031370	153 -- 170	1 -- 22	fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5-amino-6-(5-phosphoribosylamino) uracil reductase	_____________152____________________171\n_____________\|______________________\|\n5'-AAA...UCGAA____________UU________GAAGA...AAG-3'\n______________GAUAUCAAAGAA______UGGC\n______________\|\|:\|\|\|\|\|\|\|\|\|______\|\|\|\|\n______________CUGUAGUUUCUU______ACCG\n3'-UUU...UACCC____________UUCGUC____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	158 -- 164	11 -- 17	-19.3666 kcal/mol	3.04735 kcal/mol	1.54023 kcal/mol	152 171@LB@ \| \|@LB@5'-AAA...UCGAA UU GAAGA...AAG-3'@LB@ GAUAUCAAAGAA UGGC@LB@ \|\|:\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUGUAGUUUCUU ACCG@LB@3'-UUU...UACCC UUCGUC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -19.3666 kcal/mol@LB@Unfolding Energy - mRNA 3.04735 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 153 -- 170@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 11 -- 17@LB@
174	0.0127	0.2504	b1960	vsr	-15.05	0.027057	161 -- 177	1 -- 19	DNA mismatch endonuclease of very short patch repair	_____________160_________________178\n_____________\|___________________\|\n5'-UCG...CAAAA______C____________GUUGC...CCG-3'\n______________AUCAAA___AGGCGGUGGC\n______________\|\|\|\|\|\|___\|:\|\|:\|\|\|\|\|\n______________UAGUUU___UUCGUCACCG\n3'-UUU...CCCUG______CUU__________-5'\n_____________\|__________________\|\n_____________20_________________1\n	171 -- 177	1 -- 7	-22.0844 kcal/mol	5.58177 kcal/mol	1.45734 kcal/mol	160 178@LB@ \| \|@LB@5'-UCG...CAAAA C GUUGC...CCG-3'@LB@ AUCAAA AGGCGGUGGC@LB@ \|\|\|\|\|\| \|:\|\|:\|\|\|\|\|@LB@ UAGUUU UUCGUCACCG@LB@3'-UUU...CCCUG CUU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -22.0844 kcal/mol@LB@Unfolding Energy - mRNA 5.58177 kcal/mol@LB@Unfolding Energy - sRNA 1.45734 kcal/mol@LB@@LB@Position - mRNA 161 -- 177@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 1 -- 7@LB@
149	0.01096	0.2504	b3230	rpsI	-12.23	0.111717	165 -- 205	1 -- 34	30S ribosomal subunit protein S9	_____________164_______________________________________206\n_____________\|_________________________________________\|\n5'-GUG...AGCAA_______UUCUU______UAAUC____UUAU_____A____UGAAA...GUU-3'\n______________CCGCAAG_____GACAUC_____GGGA____AGGCA_UGGC\n______________\|\|:\|\|\|:_____\|\|\|\|\|\|_____:\|:\|____\|:\|\|\|_\|\|\|\|\n______________GGUGUUU_____CUGUAG_____UCUU____UUCGU_ACCG\n3'-UUU...CCCGA_______UACCC______UU________________C____-5'\n_____________\|________________________________________\|\n_____________35_______________________________________1\n	165 -- 171	28 -- 34	-26.3465 kcal/mol	9.84752 kcal/mol	4.26884 kcal/mol	164 206@LB@ \| \|@LB@5'-GUG...AGCAA UUCUU UAAUC UUAU A UGAAA...GUU-3'@LB@ CCGCAAG GACAUC GGGA AGGCA UGGC@LB@ \|\|:\|\|\|: \|\|\|\|\|\| :\|:\| \|:\|\|\| \|\|\|\|@LB@ GGUGUUU CUGUAG UCUU UUCGU ACCG@LB@3'-UUU...CCCGA UACCC UU C -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -26.3465 kcal/mol@LB@Unfolding Energy - mRNA 9.84752 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 165 -- 205@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 28 -- 34@LB@
156	0.01139	0.2504	b0197	metQ	-9.46	0.330846	169 -- 205	1 -- 33	DL-methionine transporter subunit	_____________168_____________________________________206\n_____________\|_______________________________________\|\n5'-GUG...UUCAA_____CAUAAAUA___________GAAUAA_________GUUCA...UUA-3'\n______________CACAA_________AUUGAAGAAG______GGUA_UGGC\n______________\|\|\|\|\|_________\|\|::\|\|\|\|\|:______:\|:\|_\|\|\|\|\n______________GUGUU_________UAGUUUCUUU______UCGU_ACCG\n3'-UUU...CCGAG_____UUACCCCUG____________________C____-5'\n_____________\|______________________________________\|\n_____________34_____________________________________1\n	185 -- 191	10 -- 16	-16.9822 kcal/mol	4.44131 kcal/mol	3.07861 kcal/mol	168 206@LB@ \| \|@LB@5'-GUG...UUCAA CAUAAAUA GAAUAA GUUCA...UUA-3'@LB@ CACAA AUUGAAGAAG GGUA UGGC@LB@ \|\|\|\|\| \|\|::\|\|\|\|\|: :\|:\| \|\|\|\|@LB@ GUGUU UAGUUUCUUU UCGU ACCG@LB@3'-UUU...CCGAG UUACCCCUG C -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -16.9822 kcal/mol@LB@Unfolding Energy - mRNA 4.44131 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 169 -- 205@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 10 -- 16@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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