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
2	5.107e-11	8.961e-08	b2314	dedD	-25.37	0.000001	176 -- 205	1 -- 30	membrane-anchored periplasmic protein involved in septation	_____________175_____________________________206\n_____________\|_______________________________\|\n5'-UUG...UCAUG______AUU______________________AAGUA...AUU-3'\n______________GAAGUG___GACG_CGAGGAGAAGCGGUGGC\n______________:\|\|:\|\|___\|\|\|:_\|:\|:\|\|:\|\|\|\|:\|\|\|\|\|\n______________UUUUAC___CUGU_GUUUCUUUUCGUCACCG\n3'-UUU...AGGUG______CC_____A_________________-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	199 -- 205	1 -- 7	-36.5756 kcal/mol	8.68219 kcal/mol	2.51911 kcal/mol	175 206@LB@ \| \|@LB@5'-UUG...UCAUG AUU AAGUA...AUU-3'@LB@ GAAGUG GACG CGAGGAGAAGCGGUGGC@LB@ :\|\|:\|\| \|\|\|: \|:\|:\|\|:\|\|\|\|:\|\|\|\|\|@LB@ UUUUAC CUGU GUUUCUUUUCGUCACCG@LB@3'-UUU...AGGUG CC A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -25.37 kcal/mol@LB@Hybridization Energy -36.5756 kcal/mol@LB@Unfolding Energy - mRNA 8.68219 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 176 -- 205@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 1 -- 7@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@
22	0.0008145	0.1243	b3574	yiaJ	-21.10	0.000313	196 -- 241	1 -- 32	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon	_____________195____________________________________________242\n_____________\|______________________________________________\|\n5'-CCC...ACGCG____________A_GAAGUGAUGGGAAAA________CG__A____GCAGG...UUG-3'\n______________ACAAAAUGGGGA_A_______________AAAGAGAA__AG_UGGC\n______________\|\|\|\|\|\|\|\|\|\|\|\|_\|_______________\|\|\|\|\|:\|\|__\|\|_\|\|\|\|\n______________UGUUUUACCCCU_U_______________UUUCUUUU__UC_ACCG\n3'-UUU...CGAGG____________G_AG_____________________CG_______-5'\n_____________\|_____________________________________________\|\n_____________33____________________________________________1\n	226 -- 232	9 -- 15	-30.0936 kcal/mol	6.45407 kcal/mol	2.53929 kcal/mol	195 242@LB@ \| \|@LB@5'-CCC...ACGCG A GAAGUGAUGGGAAAA CG A GCAGG...UUG-3'@LB@ ACAAAAUGGGGA A AAAGAGAA AG UGGC@LB@ \|\|\|\|\|\|\|\|\|\|\|\| \| \|\|\|\|\|:\|\| \|\| \|\|\|\|@LB@ UGUUUUACCCCU U UUUCUUUU UC ACCG@LB@3'-UUU...CGAGG G AG CG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -21.10 kcal/mol@LB@Hybridization Energy -30.0936 kcal/mol@LB@Unfolding Energy - mRNA 6.45407 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 196 -- 241@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 226 -- 232@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@
1	0	0	b3752	rbsK	-20.54	0.000534	137 -- 155	1 -- 21	ribokinase	_____________136___________________156\n_____________\|_____________________\|\n5'-GCA...GUGUA_____________________ACGCG...GUA-3'\n______________AUA_UAAAGAAAAGCAG_GGC\n______________\|:\|_:\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\n______________UGU_GUUUCUUUUCGUC_CCG\n3'-UUU...ACCCC___A_____________A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	146 -- 152	5 -- 11	-23.5677 kcal/mol	1.51892 kcal/mol	1.51103 kcal/mol	136 156@LB@ \| \|@LB@5'-GCA...GUGUA ACGCG...GUA-3'@LB@ AUA UAAAGAAAAGCAG GGC@LB@ \|:\| :\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|@LB@ UGU GUUUCUUUUCGUC CCG@LB@3'-UUU...ACCCC A A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -20.54 kcal/mol@LB@Hybridization Energy -23.5677 kcal/mol@LB@Unfolding Energy - mRNA 1.51892 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 137 -- 155@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 5 -- 11@LB@
198	0.01428	0.2531	b4393	trpR	-20.45	0.000581	86 -- 104	16 -- 34	transcriptional repressor tryptophan-binding	_____________85__________________105\n_____________\|___________________\|\n5'-GAG...GAGCG___________________UUACU...AUC-3'\n______________CCACGGAAUGGGGACGUCG\n______________\|\|\|\|::\|\|\|\|\|\|\|\|\|:\|\|:\n______________GGUGUUUUACCCCUGUAGU\n3'-UUU...CCCGA___________________UUCUU...CCG-5'\n_____________\|___________________\|\n_____________35__________________15\n	98 -- 104	16 -- 22	-32.2935 kcal/mol	7.91935 kcal/mol	3.92811 kcal/mol	85 105@LB@ \| \|@LB@5'-GAG...GAGCG UUACU...AUC-3'@LB@ CCACGGAAUGGGGACGUCG@LB@ \|\|\|\|::\|\|\|\|\|\|\|\|\|:\|\|:@LB@ GGUGUUUUACCCCUGUAGU@LB@3'-UUU...CCCGA UUCUU...CCG-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -20.45 kcal/mol@LB@Hybridization Energy -32.2935 kcal/mol@LB@Unfolding Energy - mRNA 7.91935 kcal/mol@LB@Unfolding Energy - sRNA 3.92811 kcal/mol@LB@@LB@Position - mRNA 86 -- 104@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 16 -- 22@LB@
111	0.007434	0.2348	b0103	coaE	-19.66	0.001155	224 -- 242	1 -- 25	dephospho-CoA kinase	_____________223________________________243\n_____________\|__________________________\|\n5'-UAU...UUAAC___A______________________AAGAG...AUA-3'\n______________GGG_GGCAUU_______GGCAGUGGC\n______________\|\|\|_\|:\|\|\|:_______:\|\|\|\|\|\|\|\|\n______________CCC_CUGUAG_______UCGUCACCG\n3'-UUU...UUUUA__________UUUCUUU_________-5'\n_____________\|_________________________\|\n_____________26________________________1\n	236 -- 242	1 -- 7	-28.3462 kcal/mol	6.16994 kcal/mol	2.51748 kcal/mol	223 243@LB@ \| \|@LB@5'-UAU...UUAAC A AAGAG...AUA-3'@LB@ GGG GGCAUU GGCAGUGGC@LB@ \|\|\| \|:\|\|\|: :\|\|\|\|\|\|\|\|@LB@ CCC CUGUAG UCGUCACCG@LB@3'-UUU...UUUUA UUUCUUU -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -19.66 kcal/mol@LB@Hybridization Energy -28.3462 kcal/mol@LB@Unfolding Energy - mRNA 6.16994 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 224 -- 242@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 1 -- 7@LB@
18	0.0007186	0.1243	b3657	yicJ	-19.60	0.001218	184 -- 200	5 -- 21	putative transporter	_____________183_______________201\n_____________\|_________________\|\n5'-CAG...CUAUA_________________AUGAA...UGU-3'\n______________GCAUCAAGGAAAAGCAG\n______________:\|\|\|\|\|\|:\|\|\|\|\|\|\|\|\|\n______________UGUAGUUUCUUUUCGUC\n3'-UUU...ACCCC_________________ACCG-5'\n_____________\|_________________\|\n_____________22________________4\n	194 -- 200	5 -- 11	-25.6417 kcal/mol	4.53845 kcal/mol	1.5073 kcal/mol	183 201@LB@ \| \|@LB@5'-CAG...CUAUA AUGAA...UGU-3'@LB@ GCAUCAAGGAAAAGCAG@LB@ :\|\|\|\|\|\|:\|\|\|\|\|\|\|\|\|@LB@ UGUAGUUUCUUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -19.60 kcal/mol@LB@Hybridization Energy -25.6417 kcal/mol@LB@Unfolding Energy - mRNA 4.53845 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 184 -- 200@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
5	2.356e-05	0.01653	b1123	potD	-19.53	0.001282	190 -- 207	9 -- 25	spermidine/putrescine ABC transporter periplasmic binding protein	_____________189________________208\n_____________\|__________________\|\n5'-GAC...ACACA____________U_____AAUGG...ACU-3'\n______________GGGGACGUUAAA_GAAAA\n______________\|\|\|\|\|\|:\|:\|\|\|_\|\|\|\|\|\n______________CCCCUGUAGUUU_CUUUU\n3'-UUU...UUUUA__________________CGUCACCG-5'\n_____________\|__________________\|\n_____________26_________________8\n	195 -- 201	14 -- 20	-22.5319 kcal/mol	2.32696 kcal/mol	0.671024 kcal/mol	189 208@LB@ \| \|@LB@5'-GAC...ACACA U AAUGG...ACU-3'@LB@ GGGGACGUUAAA GAAAA@LB@ \|\|\|\|\|\|:\|:\|\|\| \|\|\|\|\|@LB@ CCCCUGUAGUUU CUUUU@LB@3'-UUU...UUUUA CGUCACCG-5'@LB@ \| \|@LB@ 26 8@LB@@LB@@LB@Energy -19.53 kcal/mol@LB@Hybridization Energy -22.5319 kcal/mol@LB@Unfolding Energy - mRNA 2.32696 kcal/mol@LB@Unfolding Energy - sRNA 0.671024 kcal/mol@LB@@LB@Position - mRNA 190 -- 207@LB@Position - sRNA 9 -- 25@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 14 -- 20@LB@
44	0.002166	0.1648	b3349	slyD	-19.18	0.001707	20 -- 41	5 -- 23	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)	_____________19_____________________42\n_____________\|______________________\|\n5'-UGU...AGUGC__________UGC_________ACAAA...ACU-3'\n______________GGACAUCAGA___GAGAAGCAG\n______________\|\|\|\|\|\|\|\|:\|___\|\|:\|\|\|\|\|\|\n______________CCUGUAGUUU___CUUUUCGUC\n3'-UUU...UUACC______________________ACCG-5'\n_____________\|______________________\|\n_____________24_____________________4\n	35 -- 41	5 -- 11	-25.7728 kcal/mol	5.01574 kcal/mol	1.57523 kcal/mol	19 42@LB@ \| \|@LB@5'-UGU...AGUGC UGC ACAAA...ACU-3'@LB@ GGACAUCAGA GAGAAGCAG@LB@ \|\|\|\|\|\|\|\|:\| \|\|:\|\|\|\|\|\|@LB@ CCUGUAGUUU CUUUUCGUC@LB@3'-UUU...UUACC ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -19.18 kcal/mol@LB@Hybridization Energy -25.7728 kcal/mol@LB@Unfolding Energy - mRNA 5.01574 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 20 -- 41@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 5 -- 11@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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