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
150	0.01097	0.2504	b1878	flhE	-16.24	0.013409	257 -- 279	3 -- 25	proton seal during flagellar secretion	_____________256_____________________280\n_____________\|_______________________\|\n5'-CGU...GGGGA________G_C___C________UAGGA...AUC-3'\n______________GGGGAUGU_G_AGG_AAGUAGUG\n______________\|\|\|\|\|::\|_:_\|\|:_\|\|\|:\|\|\|\|\n______________CCCCUGUA_U_UCU_UUCGUCAC\n3'-UUU...UUUUA________G_U___U________CG-5'\n_____________\|_______________________\|\n_____________26______________________2\n	273 -- 279	3 -- 9	-26.0465 kcal/mol	7.2914 kcal/mol	2.5166 kcal/mol	256 280@LB@ \| \|@LB@5'-CGU...GGGGA G C C UAGGA...AUC-3'@LB@ GGGGAUGU G AGG AAGUAGUG@LB@ \|\|\|\|\|::\| : \|\|: \|\|\|:\|\|\|\|@LB@ CCCCUGUA U UCU UUCGUCAC@LB@3'-UUU...UUUUA G U U CG-5'@LB@ \| \|@LB@ 26 2@LB@@LB@@LB@Energy -16.24 kcal/mol@LB@Hybridization Energy -26.0465 kcal/mol@LB@Unfolding Energy - mRNA 7.2914 kcal/mol@LB@Unfolding Energy - sRNA 2.5166 kcal/mol@LB@@LB@Position - mRNA 257 -- 279@LB@Position - sRNA 3 -- 25@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 3 -- 9@LB@
103	0.006657	0.2268	b3617	kbl	-13.19	0.071337	258 -- 276	7 -- 25	glycine C-acetyltransferase	_____________257_________________277\n_____________\|___________________\|\n5'-UUU...CGGAA___UUGU____________GCAUU...AAG-3'\n______________GGG____UUAAAGAAGAGC\n______________\|\|\|____\|:\|\|\|\|\|\|:\|\|\|\n______________CCC____AGUUUCUUUUCG\n3'-UUU...UUUUA___CUGU____________UCACCG-5'\n_____________\|___________________\|\n_____________26__________________6\n	270 -- 276	7 -- 13	-19.594 kcal/mol	5.69693 kcal/mol	0.70626 kcal/mol	257 277@LB@ \| \|@LB@5'-UUU...CGGAA UUGU GCAUU...AAG-3'@LB@ GGG UUAAAGAAGAGC@LB@ \|\|\| \|:\|\|\|\|\|\|:\|\|\|@LB@ CCC AGUUUCUUUUCG@LB@3'-UUU...UUUUA CUGU UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -19.594 kcal/mol@LB@Unfolding Energy - mRNA 5.69693 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 258 -- 276@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 7 -- 13@LB@
171	0.01235	0.2504	b1092	fabD	-9.75	0.300248	258 -- 270	47 -- 59	malonyl-CoA-[acyl-carrier-protein] transacylase	_____________257___________271\n_____________\|_____________\|\n5'-AAC...UGCUG_____U_______CGAGC...UUG-3'\n______________GCUGA_AUGGCGG\n______________:\|:\|\|_\|\|\|\|\|\|\|\n______________UGGCU_UACCGCC\n3'-UUU...GAACU_____U_______CCAAC...CCG-5'\n_____________\|_____________\|\n_____________60____________46\n	264 -- 270	47 -- 53	-17.9053 kcal/mol	4.19285 kcal/mol	3.96442 kcal/mol	257 271@LB@ \| \|@LB@5'-AAC...UGCUG U CGAGC...UUG-3'@LB@ GCUGA AUGGCGG@LB@ :\|:\|\| \|\|\|\|\|\|\|@LB@ UGGCU UACCGCC@LB@3'-UUU...GAACU U CCAAC...CCG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -9.75 kcal/mol@LB@Hybridization Energy -17.9053 kcal/mol@LB@Unfolding Energy - mRNA 4.19285 kcal/mol@LB@Unfolding Energy - sRNA 3.96442 kcal/mol@LB@@LB@Position - mRNA 258 -- 270@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 47 -- 53@LB@
7	0.0001218	0.05555	b1811	yoaH	-21.30	0.000256	259 -- 293	1 -- 35	UPF0181 family protein	_____________258__________________________________294\n_____________\|____________________________________\|\n5'-ACG...GCGGA____G___C__AU____________U______C___CAGGCAA-3'\n______________UCCA_GAA_UG__GGCA_CAAGGGA_GAGCAG_GGC\n______________\|\|\|\|_:\|\|_\|\|__\|:\|\|_\|\|\|:\|:\|_:\|\|\|\|\|_\|\|\|\n______________AGGU_UUU_AC__CUGU_GUUUCUU_UUCGUC_CCG\n3'-UUU...ACCCG____G___U__CC____A______________A___-5'\n_____________\|___________________________________\|\n_____________36__________________________________1\n	276 -- 282	11 -- 17	-33.9537 kcal/mol	7.61738 kcal/mol	5.03645 kcal/mol	258 294@LB@ \| \|@LB@5'-ACG...GCGGA G C AU U C CAGGCAA-3'@LB@ UCCA GAA UG GGCA CAAGGGA GAGCAG GGC@LB@ \|\|\|\| :\|\| \|\| \|:\|\| \|\|\|:\|:\| :\|\|\|\|\| \|\|\|@LB@ AGGU UUU AC CUGU GUUUCUU UUCGUC CCG@LB@3'-UUU...ACCCG G U CC A A -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -21.30 kcal/mol@LB@Hybridization Energy -33.9537 kcal/mol@LB@Unfolding Energy - mRNA 7.61738 kcal/mol@LB@Unfolding Energy - sRNA 5.03645 kcal/mol@LB@@LB@Position - mRNA 259 -- 293@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 11 -- 17@LB@
27	0.001238	0.1512	b4045	yjbJ	-9.99	0.275707	259 -- 267	19 -- 28	stress-induced protein UPF0337 family	_____________258________268\n_____________\|__________\|\n5'-CGU...AGAGC__________AACUG...AAG-3'\n______________AAUGGGG_CA\n______________\|\|\|\|\|\|\|_\|\|\n______________UUACCCC_GU\n3'-UUU...GUGUU_______U__AGUUU...CCG-5'\n_____________\|__________\|\n_____________29_________18\n	259 -- 265	22 -- 28	-11.8839 kcal/mol	1.24365 kcal/mol	0.649553 kcal/mol	258 268@LB@ \| \|@LB@5'-CGU...AGAGC AACUG...AAG-3'@LB@ AAUGGGG CA@LB@ \|\|\|\|\|\|\| \|\|@LB@ UUACCCC GU@LB@3'-UUU...GUGUU U AGUUU...CCG-5'@LB@ \| \|@LB@ 29 18@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -11.8839 kcal/mol@LB@Unfolding Energy - mRNA 1.24365 kcal/mol@LB@Unfolding Energy - sRNA 0.649553 kcal/mol@LB@@LB@Position - mRNA 259 -- 267@LB@Position - sRNA 19 -- 28@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 22 -- 28@LB@
154	0.01125	0.2504	b3412	bioH	-12.84	0.084220	262 -- 288	1 -- 28	pimeloyl-ACP methyl ester carboxylesterase	_____________261__________________________289\n_____________\|____________________________\|\n5'-GGC...GCACG_________UGAAUGCC___________GUUGC...ACG-3'\n______________GAUGGGGAC________GAAGU_GUGGC\n______________:\|\|\|\|\|\|\|\|________:\|\|\|:_\|\|\|\|\|\n______________UUACCCCUG________UUUCG_CACCG\n3'-UUU...GUGUU_________UAGUUUCU_____U_____-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	264 -- 270	20 -- 26	-27.647 kcal/mol	12.2839 kcal/mol	2.519 kcal/mol	261 289@LB@ \| \|@LB@5'-GGC...GCACG UGAAUGCC GUUGC...ACG-3'@LB@ GAUGGGGAC GAAGU GUGGC@LB@ :\|\|\|\|\|\|\|\| :\|\|\|: \|\|\|\|\|@LB@ UUACCCCUG UUUCG CACCG@LB@3'-UUU...GUGUU UAGUUUCU U -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -12.84 kcal/mol@LB@Hybridization Energy -27.647 kcal/mol@LB@Unfolding Energy - mRNA 12.2839 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 262 -- 288@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 20 -- 26@LB@
63	0.003337	0.1851	b1453	ansP	-14.01	0.047364	263 -- 293	1 -- 34	L-asparagine transporter	_____________262_________________________________294\n_____________\|___________________________________\|\n5'-GUC...AAUGC________A__________C_________AUG___AAUCGCC-3'\n______________CCACGAAG_GGGG_UAUCA____AAAGCG___GGC\n______________\|\|\|\|:\|\|:_\|\|\|\|_:\|\|\|\|____\|\|\|\|\|:___\|\|\|\n______________GGUGUUUU_CCCC_GUAGU____UUUCGU___CCG\n3'-UUU...CCCGA________A____U_____UUCU______CA____-5'\n_____________\|__________________________________\|\n_____________35_________________________________1\n	263 -- 269	28 -- 34	-31.7064 kcal/mol	13.4305 kcal/mol	4.26884 kcal/mol	262 294@LB@ \| \|@LB@5'-GUC...AAUGC A C AUG AAUCGCC-3'@LB@ CCACGAAG GGGG UAUCA AAAGCG GGC@LB@ \|\|\|\|:\|\|: \|\|\|\| :\|\|\|\| \|\|\|\|\|: \|\|\|@LB@ GGUGUUUU CCCC GUAGU UUUCGU CCG@LB@3'-UUU...CCCGA A U UUCU CA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -31.7064 kcal/mol@LB@Unfolding Energy - mRNA 13.4305 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 263 -- 293@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 28 -- 34@LB@
80	0.004856	0.213	b1478	adhP	-8.37	0.463200	263 -- 276	48 -- 59	ethanol-active dehydrogenase/acetaldehyde-active reductase	_____________262____________277\n_____________\|______________\|\n5'-GCA...CGCUC_______CA_____AAGCC...GUU-3'\n______________ACUGAAA__UGGCG\n______________\|\|:\|\|\|\|__\|\|\|\|\|\n______________UGGCUUU__ACCGC\n3'-UUU...GAACU______________CCCAA...CCG-5'\n_____________\|______________\|\n_____________60_____________47\n	263 -- 269	53 -- 59	-14.4135 kcal/mol	2.08604 kcal/mol	3.96136 kcal/mol	262 277@LB@ \| \|@LB@5'-GCA...CGCUC CA AAGCC...GUU-3'@LB@ ACUGAAA UGGCG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ UGGCUUU ACCGC@LB@3'-UUU...GAACU CCCAA...CCG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -14.4135 kcal/mol@LB@Unfolding Energy - mRNA 2.08604 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 263 -- 276@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 53 -- 59@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@
17	0.0006839	0.1243	b1247	oppF	-10.96	0.191014	264 -- 288	1 -- 22	oligopeptide ABC transporter ATPase	_____________263________________________289\n_____________\|__________________________\|\n5'-GCG...ACUUU__A________U____AAAC______UCUGG...CGC-3'\n______________GA_AUCAAAGA__GGC____AGUGGU\n______________\|\|_\|\|\|\|\|\|\|\|__:\|\|____\|\|\|\|\|:\n______________CU_UAGUUUCU__UCG____UCACCG\n3'-UUU...UACCC__G________UU_____________-5'\n_____________\|_________________________\|\n_____________23________________________1\n	268 -- 274	12 -- 18	-19.2479 kcal/mol	6.74487 kcal/mol	1.54023 kcal/mol	263 289@LB@ \| \|@LB@5'-GCG...ACUUU A U AAAC UCUGG...CGC-3'@LB@ GA AUCAAAGA GGC AGUGGU@LB@ \|\| \|\|\|\|\|\|\|\| :\|\| \|\|\|\|\|:@LB@ CU UAGUUUCU UCG UCACCG@LB@3'-UUU...UACCC G UU -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -19.2479 kcal/mol@LB@Unfolding Energy - mRNA 6.74487 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 264 -- 288@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 12 -- 18@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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