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
19	0.000738	0.1243	b1508	hipB	-18.00	0.004180	266 -- 295	1 -- 32	antitoxin of HipAB toxin-antitoxin system	b1299 b1434	_____________265________________________________296\n_____________\|__________________________________\|\n5'-AUG...CGCCA_________CU___________C___________GAAAA-3'\n______________GCAAAAUGG__GGACG_CAGAG__GAGC__UGGC\n______________:\|\|\|\|\|\|\|\|__\|\|\|\|:_\|\|:\|\|__:\|\|\|__\|\|\|\|\n______________UGUUUUACC__CCUGU_GUUUC__UUCG__ACCG\n3'-UUU...CGAGG________________A_____UU____UC____-5'\n_____________\|_________________________________\|\n_____________33________________________________1\n	268 -- 274	24 -- 30	-30.0826 kcal/mol	9.54799 kcal/mol	2.53929 kcal/mol	265 296@LB@ \| \|@LB@5'-AUG...CGCCA CU C GAAAA-3'@LB@ GCAAAAUGG GGACG CAGAG GAGC UGGC@LB@ :\|\|\|\|\|\|\|\| \|\|\|\|: \|\|:\|\| :\|\|\| \|\|\|\|@LB@ UGUUUUACC CCUGU GUUUC UUCG ACCG@LB@3'-UUU...CGAGG A UU UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -30.0826 kcal/mol@LB@Unfolding Energy - mRNA 9.54799 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 24 -- 30@LB@
81	0.004938	0.2139	b0115	aceF	-13.95	0.048783	266 -- 289	7 -- 31	pyruvate dehydrogenase dihydrolipoyltransacetylase component E2		_____________265_________________________290\n_____________\|___________________________\|\n5'-GAU...CUGGU_________C__________UU_____CGAAC...CGC-3'\n______________CAAAGUGGG_GACA___AAG__GAAGC\n______________\|\|\|\|:\|\|\|\|_\|\|\|\|___\|\|\|__:\|\|\|\|\n______________GUUUUACCC_CUGU___UUC__UUUCG\n3'-UUU...GAGGU______________AGU___U______UCACCG-5'\n_____________\|___________________________\|\n_____________32__________________________6\n	268 -- 274	23 -- 29	-21.1287 kcal/mol	4.65658 kcal/mol	2.52208 kcal/mol	265 290@LB@ \| \|@LB@5'-GAU...CUGGU C UU CGAAC...CGC-3'@LB@ CAAAGUGGG GACA AAG GAAGC@LB@ \|\|\|\|:\|\|\|\| \|\|\|\| \|\|\| :\|\|\|\|@LB@ GUUUUACCC CUGU UUC UUUCG@LB@3'-UUU...GAGGU AGU U UCACCG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -21.1287 kcal/mol@LB@Unfolding Energy - mRNA 4.65658 kcal/mol@LB@Unfolding Energy - sRNA 2.52208 kcal/mol@LB@@LB@Position - mRNA 266 -- 289@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 23 -- 29@LB@
94	0.005808	0.2147	b0652	gltL	-13.33	0.066498	266 -- 292	1 -- 31	glutamate/aspartate ABC transporter ATPase		_____________265_____________________________293\n_____________\|_______________________________\|\n5'-CUC...UCAAC_______AAAA________C___________GGUUUGCG-3'\n______________CGAAGUG________AAGG_GAAGUGGUGGU\n______________\|:\|\|:\|\|________\|\|:\|_:\|\|\|::\|\|\|\|:\n______________GUUUUAC________UUUC_UUUCGUCACCG\n3'-UUU...GAGGU_______CCCUGUAG____U___________-5'\n_____________\|______________________________\|\n_____________32_____________________________1\n	286 -- 292	1 -- 7	-20.9442 kcal/mol	5.07032 kcal/mol	2.53929 kcal/mol	265 293@LB@ \| \|@LB@5'-CUC...UCAAC AAAA C GGUUUGCG-3'@LB@ CGAAGUG AAGG GAAGUGGUGGU@LB@ \|:\|\|:\|\| \|\|:\| :\|\|\|::\|\|\|\|:@LB@ GUUUUAC UUUC UUUCGUCACCG@LB@3'-UUU...GAGGU CCCUGUAG U -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -20.9442 kcal/mol@LB@Unfolding Energy - mRNA 5.07032 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 266 -- 292@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 1 -- 7@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@
133	0.009634	0.2504	b2551	glyA	-13.83	0.051752	272 -- 286	6 -- 21	serine hydroxymethyltransferase		_____________271______________287\n_____________\|________________\|\n5'-CAA...AAAGU________________CAUCG...UCG-3'\n______________ACGUC_AGGAAGAGCA\n______________\|\|:\|\|_\|:\|\|\|:\|\|\|\|\n______________UGUAG_UUCUUUUCGU\n3'-UUU...ACCCC_____U__________CACCG-5'\n_____________\|________________\|\n_____________22_______________5\n	280 -- 286	6 -- 12	-16.7043 kcal/mol	2.28484 kcal/mol	0.584589 kcal/mol	271 287@LB@ \| \|@LB@5'-CAA...AAAGU CAUCG...UCG-3'@LB@ ACGUC AGGAAGAGCA@LB@ \|\|:\|\| \|:\|\|\|:\|\|\|\|@LB@ UGUAG UUCUUUUCGU@LB@3'-UUU...ACCCC U CACCG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -16.7043 kcal/mol@LB@Unfolding Energy - mRNA 2.28484 kcal/mol@LB@Unfolding Energy - sRNA 0.584589 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 6 -- 12@LB@
143	0.01049	0.2504	b1004	wrbA	-9.61	0.314473	272 -- 293	1 -- 25	NAD(P)H:quinone oxidoreductase		_____________271________________________294\n_____________\|__________________________\|\n5'-UUA...GCUGA___U_________C_______A____GCUGAAG-3'\n______________GGG_GCA____AG_AAAGUGG_UGGC\n______________\|\|\|_:\|\|____\|\|_\|\|\|\|::\|_\|\|\|\|\n______________CCC_UGU____UC_UUUCGUC_ACCG\n3'-UUU...UUUUA___C___AGUU__U____________-5'\n_____________\|_________________________\|\n_____________26________________________1\n	282 -- 288	5 -- 11	-20.1219 kcal/mol	7.99134 kcal/mol	2.51748 kcal/mol	271 294@LB@ \| \|@LB@5'-UUA...GCUGA U C A GCUGAAG-3'@LB@ GGG GCA AG AAAGUGG UGGC@LB@ \|\|\| :\|\| \|\| \|\|\|\|::\| \|\|\|\|@LB@ CCC UGU UC UUUCGUC ACCG@LB@3'-UUU...UUUUA C AGUU U -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -20.1219 kcal/mol@LB@Unfolding Energy - mRNA 7.99134 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 272 -- 293@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 5 -- 11@LB@
134	0.009704	0.2504	b1444	patD	-10.55	0.224369	279 -- 297	10 -- 25	gamma-aminobutyraldehyde dehydrogenase		_____________278_________________298\n_____________\|___________________\|\n5'-UCG...CAACG_________UUACU_____UUG-3'\n______________GGGGACGUU_____GGAAA\n______________\|\|\|\|\|\|:\|:_____:\|\|\|\|\n______________CCCCUGUAG_____UCUUU\n3'-UUU...UUUUA_________UU________UCGUC...CCG-5'\n_____________\|___________________\|\n_____________26__________________9\n	281 -- 287	17 -- 23	-18.1658 kcal/mol	6.94606 kcal/mol	0.670388 kcal/mol	278 298@LB@ \| \|@LB@5'-UCG...CAACG UUACU UUG-3'@LB@ GGGGACGUU GGAAA@LB@ \|\|\|\|\|\|:\|: :\|\|\|\|@LB@ CCCCUGUAG UCUUU@LB@3'-UUU...UUUUA UU UCGUC...CCG-5'@LB@ \| \|@LB@ 26 9@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -18.1658 kcal/mol@LB@Unfolding Energy - mRNA 6.94606 kcal/mol@LB@Unfolding Energy - sRNA 0.670388 kcal/mol@LB@@LB@Position - mRNA 279 -- 297@LB@Position - sRNA 10 -- 25@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 17 -- 23@LB@
68	0.003723	0.191	b3131	agaR	-11.10	0.180958	280 -- 299	5 -- 22	transcriptional repressor of the aga regulon		_____________279__________________300\n_____________\|____________________\|\n5'-CAG...UCUGC____G________UGU____G-3'\n______________GACA_CAAGGGAG___GCAG\n______________\|\|\|\|_\|\|\|:\|:\|:___\|\|\|\|\n______________CUGU_GUUUCUUU___CGUC\n3'-UUU...UACCC____A________U______ACCG-5'\n_____________\|____________________\|\n_____________23___________________4\n	286 -- 292	10 -- 16	-17.5345 kcal/mol	4.90034 kcal/mol	1.53637 kcal/mol	279 300@LB@ \| \|@LB@5'-CAG...UCUGC G UGU G-3'@LB@ GACA CAAGGGAG GCAG@LB@ \|\|\|\| \|\|\|:\|:\|: \|\|\|\|@LB@ CUGU GUUUCUUU CGUC@LB@3'-UUU...UACCC A U ACCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -17.5345 kcal/mol@LB@Unfolding Energy - mRNA 4.90034 kcal/mol@LB@Unfolding Energy - sRNA 1.53637 kcal/mol@LB@@LB@Position - mRNA 280 -- 299@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 10 -- 16@LB@
138	0.0102	0.2504	b0830	gsiB	-12.88	0.082739	282 -- 298	1 -- 16	glutathione ABC transporter periplasmic binding protein		_____________281_______________299\n_____________\|_________________\|\n5'-GGC...CUGCC_____UGU_________GG-3'\n______________AAAGA___GGUGGUGGC\n______________\|\|\|\|\|___:\|::\|\|\|\|\|\n______________UUUCU___UCGUCACCG\n3'-UUU...UGUAG_____UU__________-5'\n_____________\|________________\|\n_____________17_______________1\n	292 -- 298	1 -- 7	-17.0557 kcal/mol	2.82856 kcal/mol	1.34555 kcal/mol	281 299@LB@ \| \|@LB@5'-GGC...CUGCC UGU GG-3'@LB@ AAAGA GGUGGUGGC@LB@ \|\|\|\|\| :\|::\|\|\|\|\|@LB@ UUUCU UCGUCACCG@LB@3'-UUU...UGUAG UU -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -17.0557 kcal/mol@LB@Unfolding Energy - mRNA 2.82856 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
75	0.00423	0.1979	b1917	yecC	-10.99	0.188691	288 -- 298	1 -- 11	putative ABC transporter ATPase		_____________287_________299\n_____________\|___________\|\n5'-CUG...CUGGC___________AA-3'\n______________GAAGUGGUGGC\n______________:\|\|\|::\|\|\|\|\|\n______________UUUCGUCACCG\n3'-UUU...UUUCU___________-5'\n_____________\|__________\|\n_____________12_________1\n	292 -- 298	1 -- 7	-16.6045 kcal/mol	4.33348 kcal/mol	1.27751 kcal/mol	287 299@LB@ \| \|@LB@5'-CUG...CUGGC AA-3'@LB@ GAAGUGGUGGC@LB@ :\|\|\|::\|\|\|\|\|@LB@ UUUCGUCACCG@LB@3'-UUU...UUUCU -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.6045 kcal/mol@LB@Unfolding Energy - mRNA 4.33348 kcal/mol@LB@Unfolding Energy - sRNA 1.27751 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 292 -- 298@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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