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
118	0.008241	0.2451	b3394	hofN	-17.25	0.007000	1 -- 22	2 -- 26	DNA catabolic putative fimbrial assembly protein	______________1________________________23\n______________\|________________________\|\n___________5'-_____________CU__________GGAUG...CCG-3'\n______________UGGGGGCG_CAAA____GGCGGUGG\n______________\|\|\|\|\|:\|:_\|\|\|\|____:\|\|:\|\|\|\|\n______________ACCCCUGU_GUUU____UCGUCACC\n3'-UUU...GUUUU________A____CUUU________G-5'\n_____________\|_________________________\|\n_____________27________________________1\n	16 -- 22	2 -- 8	-29.7277 kcal/mol	9.95926 kcal/mol	2.5184 kcal/mol	1 23@LB@ \| \|@LB@ 5'- CU GGAUG...CCG-3'@LB@ UGGGGGCG CAAA GGCGGUGG@LB@ \|\|\|\|\|:\|: \|\|\|\| :\|\|:\|\|\|\|@LB@ ACCCCUGU GUUU UCGUCACC@LB@3'-UUU...GUUUU A CUUU G-5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -17.25 kcal/mol@LB@Hybridization Energy -29.7277 kcal/mol@LB@Unfolding Energy - mRNA 9.95926 kcal/mol@LB@Unfolding Energy - sRNA 2.5184 kcal/mol@LB@@LB@Position - mRNA 1 -- 22@LB@Position - sRNA 2 -- 26@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 2 -- 8@LB@
45	0.002187	0.1648	b3391	hofQ	-14.99	0.027914	2 -- 20	1 -- 20	DNA catabolic putative fimbrial transporter	_____________1____________________21\n_____________\|____________________\|\n__________5'-C__________U_________GAGGC...UAG-3'\n______________UAUCAGGGGA_GGUAG_GGC\n______________:\|\|\|\|::\|:\|_:\|:\|\|_\|\|\|\n______________GUAGUUUCUU_UCGUC_CCG\n3'-UUU...CCCCU__________U_____A___-5'\n_____________\|___________________\|\n_____________21__________________1\n	5 -- 11	11 -- 17	-22.4478 kcal/mol	5.99969 kcal/mol	1.45855 kcal/mol	1 21@LB@ \| \|@LB@ 5'-C U GAGGC...UAG-3'@LB@ UAUCAGGGGA GGUAG GGC@LB@ :\|\|\|\|::\|:\| :\|:\|\| \|\|\|@LB@ GUAGUUUCUU UCGUC CCG@LB@3'-UUU...CCCCU U A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -14.99 kcal/mol@LB@Hybridization Energy -22.4478 kcal/mol@LB@Unfolding Energy - mRNA 5.99969 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 2 -- 20@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 11 -- 17@LB@
35	0.00168	0.1648	b2231	gyrA	-15.33	0.023033	230 -- 249	7 -- 25	DNA gyrase (type II topoisomerase) subunit A	_____________229__________________250\n_____________\|____________________\|\n5'-AGC...ACACC__UCA_______________UGAAG...CGC-3'\n______________GG___ACAUUGAGGAAGAGC\n______________\|\|___\|\|\|\|::\|:\|\|\|:\|\|\|\n______________CC___UGUAGUUUCUUUUCG\n3'-UUU...UUUUA__CC________________UCACCG-5'\n_____________\|____________________\|\n_____________26___________________6\n	243 -- 249	7 -- 13	-19.3394 kcal/mol	3.30418 kcal/mol	0.70626 kcal/mol	229 250@LB@ \| \|@LB@5'-AGC...ACACC UCA UGAAG...CGC-3'@LB@ GG ACAUUGAGGAAGAGC@LB@ \|\| \|\|\|\|::\|:\|\|\|:\|\|\|@LB@ CC UGUAGUUUCUUUUCG@LB@3'-UUU...UUUUA CC UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -15.33 kcal/mol@LB@Hybridization Energy -19.3394 kcal/mol@LB@Unfolding Energy - mRNA 3.30418 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 230 -- 249@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 7 -- 13@LB@
185	0.0132	0.2504	b2009	sbmC	-15.75	0.018057	263 -- 294	1 -- 27	DNA gyrase inhibitor	_____________262______________________________295\n_____________\|________________________________\|\n5'-CUG...GGCCC_____AACA____G___________UU__A__AGUUGA-3'\n______________GUGGG____GACG_UAAAGAAAGGC__UG_GC\n______________:\|\|\|\|____\|\|\|:_:\|\|\|\|\|\|\|:\|\|__\|\|_\|\|\n______________UACCC____CUGU_GUUUCUUUUCG__AC_CG\n3'-UUU...UGUUU_____________A___________UC_____-5'\n_____________\|_______________________________\|\n_____________28______________________________1\n	281 -- 287	7 -- 13	-27.1244 kcal/mol	8.85955 kcal/mol	2.51867 kcal/mol	262 295@LB@ \| \|@LB@5'-CUG...GGCCC AACA G UU A AGUUGA-3'@LB@ GUGGG GACG UAAAGAAAGGC UG GC@LB@ :\|\|\|\| \|\|\|: :\|\|\|\|\|\|\|:\|\| \|\| \|\|@LB@ UACCC CUGU GUUUCUUUUCG AC CG@LB@3'-UUU...UGUUU A UC -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -15.75 kcal/mol@LB@Hybridization Energy -27.1244 kcal/mol@LB@Unfolding Energy - mRNA 8.85955 kcal/mol@LB@Unfolding Energy - sRNA 2.51867 kcal/mol@LB@@LB@Position - mRNA 263 -- 294@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 7 -- 13@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@
109	0.007372	0.2348	b3701	dnaN	-13.44	0.063163	149 -- 162	9 -- 22	DNA polymerase III beta subunit	_____________148____________163\n_____________\|______________\|\n5'-GGC...GCCAC______________UUUUU...UGC-3'\n______________GAUAUCAAAGAAGA\n______________\|\|:\|\|\|\|\|\|\|\|\|:\|\n______________CUGUAGUUUCUUUU\n3'-UUU...UACCC______________CGUCACCG-5'\n_____________\|______________\|\n_____________23_____________8\n	156 -- 162	9 -- 15	-16.0152 kcal/mol	2.0875 kcal/mol	0.488786 kcal/mol	148 163@LB@ \| \|@LB@5'-GGC...GCCAC UUUUU...UGC-3'@LB@ GAUAUCAAAGAAGA@LB@ \|\|:\|\|\|\|\|\|\|\|\|:\|@LB@ CUGUAGUUUCUUUU@LB@3'-UUU...UACCC CGUCACCG-5'@LB@ \| \|@LB@ 23 8@LB@@LB@@LB@Energy -13.44 kcal/mol@LB@Hybridization Energy -16.0152 kcal/mol@LB@Unfolding Energy - mRNA 2.0875 kcal/mol@LB@Unfolding Energy - sRNA 0.488786 kcal/mol@LB@@LB@Position - mRNA 149 -- 162@LB@Position - sRNA 9 -- 22@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 9 -- 15@LB@
50	0.002349	0.1648	b2040	rfbD	-20.63	0.000491	127 -- 157	3 -- 32	dTDP-L-rhamnose synthase NAD(P)-dependent dTDP-4-dehydrorhamnose reductase subunit	_____________126______________________________158\n_____________\|________________________________\|\n5'-GAU...CCAAU__________UU____AUGU____________CCUAU...CUA-3'\n______________ACAAAAUGGG__GAUA_____GAAAAGUGGUG\n______________\|\|\|\|\|\|\|\|\|\|__\|\|:\|_____\|\|\|\|\|\|::\|\|\|\n______________UGUUUUACCC__CUGU_____CUUUUCGUCAC\n3'-UUU...CGAGG________________AGUUU___________CG-5'\n_____________\|________________________________\|\n_____________33_______________________________2\n	151 -- 157	3 -- 9	-27.2371 kcal/mol	4.0691 kcal/mol	2.53925 kcal/mol	126 158@LB@ \| \|@LB@5'-GAU...CCAAU UU AUGU CCUAU...CUA-3'@LB@ ACAAAAUGGG GAUA GAAAAGUGGUG@LB@ \|\|\|\|\|\|\|\|\|\| \|\|:\| \|\|\|\|\|\|::\|\|\|@LB@ UGUUUUACCC CUGU CUUUUCGUCAC@LB@3'-UUU...CGAGG AGUUU CG-5'@LB@ \| \|@LB@ 33 2@LB@@LB@@LB@Energy -20.63 kcal/mol@LB@Hybridization Energy -27.2371 kcal/mol@LB@Unfolding Energy - mRNA 4.0691 kcal/mol@LB@Unfolding Energy - sRNA 2.53925 kcal/mol@LB@@LB@Position - mRNA 127 -- 157@LB@Position - sRNA 3 -- 32@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 3 -- 9@LB@
121	0.008566	0.2484	b3466	yhhL	-13.33	0.066537	119 -- 150	1 -- 32	DUF1145 family protein	_____________118_________________________________151\n_____________\|___________________________________\|\n5'-GUU...UUCCA_____C___UCAUU_____________________GGGUC...UUA-3'\n______________GCAAA_UGG_____ACAUC_GGGAAAA__AGUGGC\n______________:\|\|\|\|_\|\|\|_____\|\|\|\|\|_::\|\|\|\|\|__\|\|\|\|\|\|\n______________UGUUU_ACC_____UGUAG_UUCUUUU__UCACCG\n3'-UUU...CGAGG_____U___CC________U_______CG______-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	138 -- 144	9 -- 15	-23.4834 kcal/mol	7.61069 kcal/mol	2.53929 kcal/mol	118 151@LB@ \| \|@LB@5'-GUU...UUCCA C UCAUU GGGUC...UUA-3'@LB@ GCAAA UGG ACAUC GGGAAAA AGUGGC@LB@ :\|\|\|\| \|\|\| \|\|\|\|\| ::\|\|\|\|\| \|\|\|\|\|\|@LB@ UGUUU ACC UGUAG UUCUUUU UCACCG@LB@3'-UUU...CGAGG U CC U CG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -23.4834 kcal/mol@LB@Unfolding Energy - mRNA 7.61069 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 119 -- 150@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 9 -- 15@LB@
51	0.00253	0.1729	b0699	ybfA	-18.06	0.004001	182 -- 204	2 -- 32	DUF2517 family protein	_____________181_____________________________205\n_____________\|_______________________________\|\n5'-AUG...UAGAU_______________________________AACUC...GGA-3'\n______________ACAAAA_GGGG______GAGAAAAGUA_UGG\n______________\|\|\|\|\|\|_\|\|\|\|______:\|\|\|\|\|\|\|:\|_\|\|\|\n______________UGUUUU_CCCC______UUCUUUUCGU_ACC\n3'-UUU...CGAGG______A____UGUAGU__________C___G-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	195 -- 201	6 -- 12	-23.7835 kcal/mol	3.18782 kcal/mol	2.53929 kcal/mol	181 205@LB@ \| \|@LB@5'-AUG...UAGAU AACUC...GGA-3'@LB@ ACAAAA GGGG GAGAAAAGUA UGG@LB@ \|\|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|:\| \|\|\|@LB@ UGUUUU CCCC UUCUUUUCGU ACC@LB@3'-UUU...CGAGG A UGUAGU C G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -18.06 kcal/mol@LB@Hybridization Energy -23.7835 kcal/mol@LB@Unfolding Energy - mRNA 3.18782 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 182 -- 204@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 6 -- 12@LB@
194	0.01408	0.2529	b0952	pqiC	-11.52	0.151794	181 -- 195	48 -- 61	DUF330 family putative lipoprotein	_____________180_____________196\n_____________\|_______________\|\n5'-ACG...AUCCA_________AG____AAACA...GCG-3'\n______________GAGCCGAAG__GGCG\n______________\|\|:\|\|\|\|\|:__\|\|\|\|\n______________CUUGGCUUU__CCGC\n3'-UUU...UGGAA_________A_____CCCAA...CCG-5'\n_____________\|_______________\|\n_____________62______________47\n	183 -- 189	53 -- 59	-21.1549 kcal/mol	5.66908 kcal/mol	3.96136 kcal/mol	180 196@LB@ \| \|@LB@5'-ACG...AUCCA AG AAACA...GCG-3'@LB@ GAGCCGAAG GGCG@LB@ \|\|:\|\|\|\|\|: \|\|\|\|@LB@ CUUGGCUUU CCGC@LB@3'-UUU...UGGAA A CCCAA...CCG-5'@LB@ \| \|@LB@ 62 47@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -21.1549 kcal/mol@LB@Unfolding Energy - mRNA 5.66908 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 181 -- 195@LB@Position - sRNA 48 -- 61@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 53 -- 59@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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