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	Additional homologs
131	0.009354	0.2491	b4478	dgoD	-14.24	0.041949	180 -- 199	1 -- 22	D-galactonate dehydratase		_____________179____________________200\n_____________\|______________________\|\n5'-AAA...GUUAA_____AUC______________AAUGA...UGA-3'\n______________GGCGU____GAGAGGCAGUG_C\n______________\|:\|:\|____\|\|:\|:\|\|\|\|\|\|_\|\n______________CUGUA____CUUUUCGUCAC_G\n3'-UUU...UACCC_____GUUU___________C_-5'\n_____________\|_____________________\|\n_____________23____________________1\n	192 -- 198	3 -- 9	-21.1696 kcal/mol	5.38995 kcal/mol	1.54023 kcal/mol	179 200@LB@ \| \|@LB@5'-AAA...GUUAA AUC AAUGA...UGA-3'@LB@ GGCGU GAGAGGCAGUG C@LB@ \|:\|:\| \|\|:\|:\|\|\|\|\|\| \|@LB@ CUGUA CUUUUCGUCAC G@LB@3'-UUU...UACCC GUUU C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -21.1696 kcal/mol@LB@Unfolding Energy - mRNA 5.38995 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 180 -- 199@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 3 -- 9@LB@
130	0.009344	0.2491	b2840	ygeA	-9.74	0.301486	266 -- 295	2 -- 29	Asp/Glu_racemase family protein		_____________265____________________________296\n_____________\|______________________________\|\n5'-AAA...UUGAU_____AA_________C__C___UU_____GCUUC-3'\n______________AAAUG__GGCAUUAAA_AG_GGC__GGUGG\n______________\|\|\|\|\|__\|:\|\|\|:\|\|\|_\|:_:\|\|__:\|\|\|\|\n______________UUUAC__CUGUAGUUU_UU_UCG__UCACC\n3'-UUU...GGUGU_____CC_________C__U__________G-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	275 -- 281	14 -- 20	-20.8158 kcal/mol	8.56062 kcal/mol	2.51906 kcal/mol	265 296@LB@ \| \|@LB@5'-AAA...UUGAU AA C C UU GCUUC-3'@LB@ AAAUG GGCAUUAAA AG GGC GGUGG@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\| \|: :\|\| :\|\|\|\|@LB@ UUUAC CUGUAGUUU UU UCG UCACC@LB@3'-UUU...GGUGU CC C U G-5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -20.8158 kcal/mol@LB@Unfolding Energy - mRNA 8.56062 kcal/mol@LB@Unfolding Energy - sRNA 2.51906 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 2 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 14 -- 20@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@
172	0.01269	0.2504	b0571	cusR	-10.48	0.230388	14 -- 48	1 -- 33	response regulator in two-component regulatory system with CusS	b1969	_____________13___________________________________49\n_____________\|____________________________________\|\n5'-AGC...GGCCA__________CA__A___UAC__________UA___UCAUA...GGC-3'\n______________CACAAAAUGG__GA_GUU___AAGGAGA_CA__GGC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|_:\|:___\|\|\|:\|:\|_\|\|__\|\|\|\n______________GUGUUUUACC__CU_UAG___UUCUUUU_GU__CCG\n3'-UUU...CCGAG__________C___G___U_________C__CA___-5'\n_____________\|___________________________________\|\n_____________34__________________________________1\n	35 -- 41	9 -- 15	-22.821 kcal/mol	9.26274 kcal/mol	3.07861 kcal/mol	13 49@LB@ \| \|@LB@5'-AGC...GGCCA CA A UAC UA UCAUA...GGC-3'@LB@ CACAAAAUGG GA GUU AAGGAGA CA GGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\| :\|: \|\|\|:\|:\| \|\| \|\|\|@LB@ GUGUUUUACC CU UAG UUCUUUU GU CCG@LB@3'-UUU...CCGAG C G U C CA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -22.821 kcal/mol@LB@Unfolding Energy - mRNA 9.26274 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 14 -- 48@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 9 -- 15@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@
146	0.01079	0.2504	b2453	eutG	-16.22	0.013596	18 -- 37	1 -- 22	ethanol dehydrogenase involved in ethanolamine utilization; aldehyde reductase		_____________17_____________________38\n_____________\|______________________\|\n5'-GGC...CGCCC_____AUU______________AUUAC...GUC-3'\n______________GGCAU____GAAGGGCAG_GGC\n______________\|:\|\|\|____\|\|\|::\|\|\|\|_\|\|\|\n______________CUGUA____CUUUUCGUC_CCG\n3'-UUU...UACCC_____GUUU_________A___-5'\n_____________\|_____________________\|\n_____________23____________________1\n	28 -- 34	5 -- 11	-23.1742 kcal/mol	5.41796 kcal/mol	1.54023 kcal/mol	17 38@LB@ \| \|@LB@5'-GGC...CGCCC AUU AUUAC...GUC-3'@LB@ GGCAU GAAGGGCAG GGC@LB@ \|:\|\|\| \|\|\|::\|\|\|\| \|\|\|@LB@ CUGUA CUUUUCGUC CCG@LB@3'-UUU...UACCC GUUU A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -23.1742 kcal/mol@LB@Unfolding Energy - mRNA 5.41796 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 18 -- 37@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 5 -- 11@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@
139	0.01022	0.2504	b3163	nlpI	-13.31	0.067339	19 -- 42	4 -- 21	lipoprotein involved in osmotic sensitivity and filamentation		_____________18_______________________43\n_____________\|________________________\|\n5'-AGG...UCUGA___________GCGACU_______CUCAA...CAU-3'\n______________GCAUUAAAGAA______GAGCAGU\n______________:\|\|\|:\|\|\|\|\|\|______:\|\|\|\|\|\|\n______________UGUAGUUUCUU______UUCGUCA\n3'-UUU...ACCCC________________________CCG-5'\n_____________\|________________________\|\n_____________22_______________________3\n	36 -- 42	4 -- 10	-18.4935 kcal/mol	3.67449 kcal/mol	1.51 kcal/mol	18 43@LB@ \| \|@LB@5'-AGG...UCUGA GCGACU CUCAA...CAU-3'@LB@ GCAUUAAAGAA GAGCAGU@LB@ :\|\|\|:\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ UGUAGUUUCUU UUCGUCA@LB@3'-UUU...ACCCC CCG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -18.4935 kcal/mol@LB@Unfolding Energy - mRNA 3.67449 kcal/mol@LB@Unfolding Energy - sRNA 1.51 kcal/mol@LB@@LB@Position - mRNA 19 -- 42@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 4 -- 10@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@
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@

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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