Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
163	0.006379	0.1377	b2210	mqo	-11.85	0.037664	161 -- 168	1 -- 8	malate dehydrogenase FAD/NAD(P)-binding domain	_____________160______169\n_____________\|________\|\n5'-GGC...AAAUC________AAUAA...AUG-3'\n______________UCACCUGC\n______________\|\|\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	162 -- 168	1 -- 7	-15.6271 kcal/mol	1.41654 kcal/mol	2.36381 kcal/mol	160 169@LB@ \| \|@LB@5'-GGC...AAAUC AAUAA...AUG-3'@LB@ UCACCUGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.85 kcal/mol@LB@Hybridization Energy -15.6271 kcal/mol@LB@Unfolding Energy - mRNA 1.41654 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 161 -- 168@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 1 -- 7@LB@
121	0.004137	0.1205	b0353	mhpT	-11.58	0.044392	170 -- 179	1 -- 10	3-hydroxyphenylpropionic transporter	_____________169________180\n_____________\|__________\|\n5'-CGG...UCGCG__________ACUCG...CGG-3'\n______________AUUCACCUGC\n______________\|\|\|\|\|\|\|\|\|\|\n______________UAAGUGGACG\n3'-UUU...CAACG__________-5'\n_____________\|_________\|\n_____________11________1\n	173 -- 179	1 -- 7	-16.6324 kcal/mol	2.26547 kcal/mol	2.7891 kcal/mol	169 180@LB@ \| \|@LB@5'-CGG...UCGCG ACUCG...CGG-3'@LB@ AUUCACCUGC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UAAGUGGACG@LB@3'-UUU...CAACG -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -16.6324 kcal/mol@LB@Unfolding Energy - mRNA 2.26547 kcal/mol@LB@Unfolding Energy - sRNA 2.7891 kcal/mol@LB@@LB@Position - mRNA 170 -- 179@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
85	0.002164	0.08969	b0910	cmk	-11.54	0.045559	249 -- 300	1 -- 56	cytidylate kinase	_____________248________________________________________________________300\n_____________\|__________________________________________________________\|\n5'-CCG...GUGCA_____________CCUU_________G______G__GGAA________AUGG_______-3'\n______________GGGA___AAGGCA_______GUGUAA_G_CUAU_GC____GCGUUGCA____CAUCUGC\n______________:\|\|\|___\|\|\|:\|\|_______\|:\|:\|\|_\|_\|:\|\|_\|\|____:\|\|\|\|\|\|\|____\|\|:\|\|\|\|\n______________UCCU___UUCUGU_______CGCGUU_C_GGUA_CG____UGCAACGU____GUGGACG\n3'-UUU...UUUUU____UCA______UAUACCU______G_G____G__AAC_________AA_________-5'\n_____________\|__________________________________________________________\|\n_____________57_________________________________________________________1\n	294 -- 300	1 -- 7	-44.7718 kcal/mol	16.3932 kcal/mol	16.8439 kcal/mol	248 300@LB@ \| \|@LB@5'-CCG...GUGCA CCUU G G GGAA AUGG -3'@LB@ GGGA AAGGCA GUGUAA G CUAU GC GCGUUGCA CAUCUGC@LB@ :\|\|\| \|\|\|:\|\| \|:\|:\|\| \| \|:\|\| \|\| :\|\|\|\|\|\|\| \|\|:\|\|\|\|@LB@ UCCU UUCUGU CGCGUU C GGUA CG UGCAACGU GUGGACG@LB@3'-UUU...UUUUU UCA UAUACCU G G G AAC AA -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -11.54 kcal/mol@LB@Hybridization Energy -44.7718 kcal/mol@LB@Unfolding Energy - mRNA 16.3932 kcal/mol@LB@Unfolding Energy - sRNA 16.8439 kcal/mol@LB@@LB@Position - mRNA 249 -- 300@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 1 -- 7@LB@
16	3.593e-05	0.007912	b2294	yfbU	-10.97	0.063921	276 -- 297	1 -- 22	UPF0304 family protein	_____________275____________________298\n_____________\|______________________\|\n5'-GCA...CAAAU___GA_____ACCG________AAA-3'\n______________GCU__ACGUU____UCGCCUGC\n______________\|\|\|__\|\|\|\|\|____\|\|:\|\|\|\|\|\n______________CGA__UGCAA____AGUGGACG\n3'-UUU...GGUAG___AC_____CGUA________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	291 -- 297	1 -- 7	-25.1893 kcal/mol	6.12655 kcal/mol	8.09964 kcal/mol	275 298@LB@ \| \|@LB@5'-GCA...CAAAU GA ACCG AAA-3'@LB@ GCU ACGUU UCGCCUGC@LB@ \|\|\| \|\|\|\|\| \|\|:\|\|\|\|\|@LB@ CGA UGCAA AGUGGACG@LB@3'-UUU...GGUAG AC CGUA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.97 kcal/mol@LB@Hybridization Energy -25.1893 kcal/mol@LB@Unfolding Energy - mRNA 6.12655 kcal/mol@LB@Unfolding Energy - sRNA 8.09964 kcal/mol@LB@@LB@Position - mRNA 276 -- 297@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 1 -- 7@LB@
155	0.006038	0.137	b4374	yjjG	-10.88	0.067155	203 -- 266	1 -- 54	dUMP phosphatase	_____________202_____________________________________________________________________267\n_____________\|_______________________________________________________________________\|\n5'-CUG...AUAAU__________________UUUUCUUU______G__GAAA____GUUUACCUU____U___________G__CUGCA...CCU-3'\n______________GAAGUGGGAC____UGGA________GAUGCC_AU____CGCU_________UGAC____CAUUCACC_GC\n______________\|\|\|\|\|::\|\|\|____\|\|\|\|________:\|:\|\|\|_\|\|____\|\|\|\|_________\|\|\|\|____\|\|\|\|\|\|\|\|_\|\|\n______________CUUCAUUCUG____ACCU________UUGCGG_UA____GCGA_________ACUG____GUAAGUGG_CG\n3'-UUU...UUUUC__________UUAU____CGCG__________G_______________________CAAC________A__-5'\n_____________\|______________________________________________________________________\|\n_____________55_____________________________________________________________________1\n	257 -- 263	4 -- 10	-41.6423 kcal/mol	13.9643 kcal/mol	16.8 kcal/mol	202 267@LB@ \| \|@LB@5'-CUG...AUAAU UUUUCUUU G GAAA GUUUACCUU U G CUGCA...CCU-3'@LB@ GAAGUGGGAC UGGA GAUGCC AU CGCU UGAC CAUUCACC GC@LB@ \|\|\|\|\|::\|\|\| \|\|\|\| :\|:\|\|\| \|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|@LB@ CUUCAUUCUG ACCU UUGCGG UA GCGA ACUG GUAAGUGG CG@LB@3'-UUU...UUUUC UUAU CGCG G CAAC A -5'@LB@ \| \|@LB@ 55 1@LB@@LB@@LB@Energy -10.88 kcal/mol@LB@Hybridization Energy -41.6423 kcal/mol@LB@Unfolding Energy - mRNA 13.9643 kcal/mol@LB@Unfolding Energy - sRNA 16.8 kcal/mol@LB@@LB@Position - mRNA 203 -- 266@LB@Position - sRNA 1 -- 54@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 4 -- 10@LB@
32	0.0001844	0.0203	b0006	yaaA	-10.88	0.067423	215 -- 223	1 -- 9	peroxide resistance protein lowers intracellular iron	_____________214_______224\n_____________\|_________\|\n5'-UUC...CUUAU_________GAAAA...AGU-3'\n______________UUCACCUGC\n______________\|\|\|\|\|\|\|\|\|\n______________AAGUGGACG\n3'-UUU...AACGU_________-5'\n_____________\|________\|\n_____________10_______1\n	217 -- 223	1 -- 7	-15.2887 kcal/mol	2.04449 kcal/mol	2.37317 kcal/mol	214 224@LB@ \| \|@LB@5'-UUC...CUUAU GAAAA...AGU-3'@LB@ UUCACCUGC@LB@ \|\|\|\|\|\|\|\|\|@LB@ AAGUGGACG@LB@3'-UUU...AACGU -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -10.88 kcal/mol@LB@Hybridization Energy -15.2887 kcal/mol@LB@Unfolding Energy - mRNA 2.04449 kcal/mol@LB@Unfolding Energy - sRNA 2.37317 kcal/mol@LB@@LB@Position - mRNA 215 -- 223@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 1 -- 7@LB@
135	0.00505	0.1318	b0918	kdsB	-10.75	0.072320	21 -- 54	1 -- 42	3-deoxy-manno-octulosonate cytidylyltransferase	_____________20_________________________________________55\n_____________\|__________________________________________\|\n5'-CCC...GGAAC______U____U______________AAU_____________CCGGU...UUC-3'\n______________UAUGGA___CA_CGUC___UGCUUGA_____CAUU_GCCUGC\n______________\|\|\|\|\|\|___\|\|_\|\|:\|___:\|\|\|\|\|\|_____\|\|\|\|_:\|\|\|\|\|\n______________AUACCU___GU_GCGG___GCGAACU_____GUAA_UGGACG\n3'-UUU...CUGUU______CGC__U____GUA_______GCAAC____G______-5'\n_____________\|_________________________________________\|\n_____________43________________________________________1\n	35 -- 41	17 -- 23	-30.6746 kcal/mol	4.6323 kcal/mol	15.293 kcal/mol	20 55@LB@ \| \|@LB@5'-CCC...GGAAC U U AAU CCGGU...UUC-3'@LB@ UAUGGA CA CGUC UGCUUGA CAUU GCCUGC@LB@ \|\|\|\|\|\| \|\| \|\|:\| :\|\|\|\|\|\| \|\|\|\| :\|\|\|\|\|@LB@ AUACCU GU GCGG GCGAACU GUAA UGGACG@LB@3'-UUU...CUGUU CGC U GUA GCAAC G -5'@LB@ \| \|@LB@ 43 1@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -30.6746 kcal/mol@LB@Unfolding Energy - mRNA 4.6323 kcal/mol@LB@Unfolding Energy - sRNA 15.293 kcal/mol@LB@@LB@Position - mRNA 21 -- 54@LB@Position - sRNA 1 -- 42@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 17 -- 23@LB@
150	0.005897	0.1368	b0887	cydD	-10.72	0.073556	183 -- 190	1 -- 8	glutathione/cysteine ABC transporter export permease/ATPase	_____________182______191\n_____________\|________\|\n5'-AUU...AUAAC________UAAGC...UGA-3'\n______________UCACCUGC\n______________\|\|\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	184 -- 190	1 -- 7	-15.001 kcal/mol	1.91816 kcal/mol	2.36381 kcal/mol	182 191@LB@ \| \|@LB@5'-AUU...AUAAC UAAGC...UGA-3'@LB@ UCACCUGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -15.001 kcal/mol@LB@Unfolding Energy - mRNA 1.91816 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 183 -- 190@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 1 -- 7@LB@
82	0.001946	0.08273	b2661	gabD	-10.13	0.102437	19 -- 25	1 -- 7	succinate-semialdehyde dehydrogenase I NADP-dependent	_____________18______26\n_____________\|_______\|\n5'-CAC...AUCCA_______AAUGC...CGG-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	19 -- 25	1 -- 7	-13.7555 kcal/mol	1.28845 kcal/mol	2.34039 kcal/mol	18 26@LB@ \| \|@LB@5'-CAC...AUCCA AAUGC...CGG-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -13.7555 kcal/mol@LB@Unfolding Energy - mRNA 1.28845 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 19 -- 25@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 1 -- 7@LB@
162	0.006351	0.1377	b1869	yecN	-10.06	0.106335	266 -- 273	1 -- 8	MAPEG family inner membrane protein	_____________265______274\n_____________\|________\|\n5'-UCA...GUCGU________GAAUG...GCG-3'\n______________UCGCCUGC\n______________\|\|:\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	267 -- 273	1 -- 7	-14.5941 kcal/mol	2.17055 kcal/mol	2.36381 kcal/mol	265 274@LB@ \| \|@LB@5'-UCA...GUCGU GAAUG...GCG-3'@LB@ UCGCCUGC@LB@ \|\|:\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.06 kcal/mol@LB@Hybridization Energy -14.5941 kcal/mol@LB@Unfolding Energy - mRNA 2.17055 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 266 -- 273@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@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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