Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
53	0.002649	0.1727	b2289	lrhA	-9.83	0.149509	112 -- 119	68 -- 75	transcriptional repressor of flagellar motility and chemotaxis genes		_____________111______120\n_____________\|________\|\n5'-CUG...AAACU________GGCAC...CCG-3'\n______________GCCAGGGA\n______________:\|\|\|\|\|\|\|\n______________UGGUCCCU\n3'-UUU...GGUUG________UUAGA...GUG-5'\n_____________\|________\|\n_____________76_______67\n	113 -- 119	68 -- 74	-14.981 kcal/mol	1.464 kcal/mol	3.68273 kcal/mol	111 120@LB@ \| \|@LB@5'-CUG...AAACU GGCAC...CCG-3'@LB@ GCCAGGGA@LB@ :\|\|\|\|\|\|\|@LB@ UGGUCCCU@LB@3'-UUU...GGUUG UUAGA...GUG-5'@LB@ \| \|@LB@ 76 67@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -14.981 kcal/mol@LB@Unfolding Energy - mRNA 1.464 kcal/mol@LB@Unfolding Energy - sRNA 3.68273 kcal/mol@LB@@LB@Position - mRNA 112 -- 119@LB@Position - sRNA 68 -- 75@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 68 -- 74@LB@
51	0.002608	0.1727	b2299	yfcD	-9.22	0.194301	162 -- 171	49 -- 58	putative NUDIX hydrolase		_____________161________172\n_____________\|__________\|\n5'-AGA...CAAAA__________GAGCG...AGU-3'\n______________UGCGCCGUAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________ACGCGGCAUU\n3'-UUU...AACCG__________UAAUA...GUG-5'\n_____________\|__________\|\n_____________59_________48\n	165 -- 171	49 -- 55	-16.7903 kcal/mol	2.6527 kcal/mol	4.92198 kcal/mol	161 172@LB@ \| \|@LB@5'-AGA...CAAAA GAGCG...AGU-3'@LB@ UGCGCCGUAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ ACGCGGCAUU@LB@3'-UUU...AACCG UAAUA...GUG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -16.7903 kcal/mol@LB@Unfolding Energy - mRNA 2.6527 kcal/mol@LB@Unfolding Energy - sRNA 4.92198 kcal/mol@LB@@LB@Position - mRNA 162 -- 171@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 49 -- 55@LB@
40	0.002113	0.1727	b2314	dedD	-12.04	0.056230	10 -- 25	1 -- 19	membrane-anchored periplasmic protein involved in septation		_____________9___________________26\n_____________\|___________________\|\n5'-UUG...GCGCC____GAA____________GGUGC...AUU-3'\n______________ACUG______GGGCCGCGC\n______________\|\|\|\|______:\|\|\|\|\|\|:\|\n______________UGAC______UCCGGCGUG\n3'-UUU...UGUCG____AAAAAG_________-5'\n_____________\|__________________\|\n_____________20_________________1\n	19 -- 25	1 -- 7	-21.4331 kcal/mol	3.12458 kcal/mol	6.26391 kcal/mol	9 26@LB@ \| \|@LB@5'-UUG...GCGCC GAA GGUGC...AUU-3'@LB@ ACUG GGGCCGCGC@LB@ \|\|\|\| :\|\|\|\|\|\|:\|@LB@ UGAC UCCGGCGUG@LB@3'-UUU...UGUCG AAAAAG -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.04 kcal/mol@LB@Hybridization Energy -21.4331 kcal/mol@LB@Unfolding Energy - mRNA 3.12458 kcal/mol@LB@Unfolding Energy - sRNA 6.26391 kcal/mol@LB@@LB@Position - mRNA 10 -- 25@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 1 -- 7@LB@
69	0.003463	0.1727	b2346	mlaA	-10.50	0.111973	167 -- 195	66 -- 86	ABC transporter maintaining OM lipid asymmetry OM lipoprotein component		_____________166___________________________196\n_____________\|_____________________________\|\n5'-GCG...GGCAA_____AUAA____UAAAAAAA________CAUUU...AAG-3'\n______________ACUGC____GCCA________CAGGGAGA\n______________\|\|\|\|\|____\|\|\|\|________\|\|\|\|\|\|:\|\n______________UGACG____CGGU________GUCCCUUU\n3'-UUU...GCUUA_____________UGUG____________AGAAC...GUG-5'\n_____________\|_____________________________\|\n_____________87____________________________65\n	189 -- 195	66 -- 72	-21.8219 kcal/mol	3.94189 kcal/mol	7.38216 kcal/mol	166 196@LB@ \| \|@LB@5'-GCG...GGCAA AUAA UAAAAAAA CAUUU...AAG-3'@LB@ ACUGC GCCA CAGGGAGA@LB@ \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ UGACG CGGU GUCCCUUU@LB@3'-UUU...GCUUA UGUG AGAAC...GUG-5'@LB@ \| \|@LB@ 87 65@LB@@LB@@LB@Energy -10.50 kcal/mol@LB@Hybridization Energy -21.8219 kcal/mol@LB@Unfolding Energy - mRNA 3.94189 kcal/mol@LB@Unfolding Energy - sRNA 7.38216 kcal/mol@LB@@LB@Position - mRNA 167 -- 195@LB@Position - sRNA 66 -- 86@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 66 -- 72@LB@
169	0.01004	0.2071	b2384	ypdE	-12.38	0.048278	93 -- 137	31 -- 75	aminopeptidase	b4305 b3898	_____________92______________________________________________138\n_____________\|_______________________________________________\|\n5'-AUU...UAUUU_______C__GGG____G_____AUCG___A_______C________CCCGC...UGC-3'\n______________GCCAGGG_AA____GGC_UGCGC____AAG_UGUUGUG_UG_GUUAC\n______________:\|\|\|\|\|\|_\|\|____\|\|\|_\|\|\|\|\|____\|\|:_\|:\|\|:\|\|_\|\|_\|\|\|\|\|\n______________UGGUCCC_UU____CCG_ACGCG____UUU_AUAAUAC_AC_CAAUG\n3'-UUU...GGUUG_______U__AGAA_________GCA____A_______U__U_____UUCCC...GUG-5'\n_____________\|_______________________________________________\|\n_____________76______________________________________________30\n	93 -- 99	69 -- 75	-40.1479 kcal/mol	18.4667 kcal/mol	9.29858 kcal/mol	92 138@LB@ \| \|@LB@5'-AUU...UAUUU C GGG G AUCG A C CCCGC...UGC-3'@LB@ GCCAGGG AA GGC UGCGC AAG UGUUGUG UG GUUAC@LB@ :\|\|\|\|\|\| \|\| \|\|\| \|\|\|\|\| \|\|: \|:\|\|:\|\| \|\| \|\|\|\|\|@LB@ UGGUCCC UU CCG ACGCG UUU AUAAUAC AC CAAUG@LB@3'-UUU...GGUUG U AGAA GCA A U U UUCCC...GUG-5'@LB@ \| \|@LB@ 76 30@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -40.1479 kcal/mol@LB@Unfolding Energy - mRNA 18.4667 kcal/mol@LB@Unfolding Energy - sRNA 9.29858 kcal/mol@LB@@LB@Position - mRNA 93 -- 137@LB@Position - sRNA 31 -- 75@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 69 -- 75@LB@
77	0.00398	0.182	b2411	ligA	-14.36	0.019662	79 -- 95	70 -- 86	DNA ligase NAD(+)-dependent		_____________78________________96\n_____________\|_________________\|\n5'-GCA...CAGAA_______G_________ACAUC...CUG-3'\n______________AUUGCGC_AGUACCAGG\n______________\|:\|\|\|\|\|_\|::\|\|\|\|\|\|\n______________UGACGCG_UUGUGGUCC\n3'-UUU...GCUUA_______G_________CUUUA...GUG-5'\n_____________\|_________________\|\n_____________87________________69\n	89 -- 95	70 -- 76	-25.4632 kcal/mol	3.82569 kcal/mol	7.27772 kcal/mol	78 96@LB@ \| \|@LB@5'-GCA...CAGAA G ACAUC...CUG-3'@LB@ AUUGCGC AGUACCAGG@LB@ \|:\|\|\|\|\| \|::\|\|\|\|\|\|@LB@ UGACGCG UUGUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -25.4632 kcal/mol@LB@Unfolding Energy - mRNA 3.82569 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 79 -- 95@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 70 -- 76@LB@
177	0.01048	0.208	b2416	ptsI	-10.21	0.127224	180 -- 212	6 -- 36	PEP-protein phosphotransferase of PTS system (enzyme I)		_____________179________________________________213\n_____________\|__________________________________\|\n5'-GUG...AAAUC___C_____UAA____G___UA__A_________AUUUU...CCG-3'\n______________AGU_ACAAG___GGUA_GGU__UG__UUUCAGGC\n______________\|\|\|_\|\|\|\|\|___\|\|:\|_:\|:__\|\|__\|\|\|\|\|\|\|\|\n______________UCA_UGUUC___CCGU_UCG__AC__AAAGUCCG\n3'-UUU...ACUAC___A____________G___UG__AA________GCGUG-5'\n_____________\|__________________________________\|\n_____________37_________________________________5\n	206 -- 212	6 -- 12	-27.3223 kcal/mol	5.11839 kcal/mol	11.9979 kcal/mol	179 213@LB@ \| \|@LB@5'-GUG...AAAUC C UAA G UA A AUUUU...CCG-3'@LB@ AGU ACAAG GGUA GGU UG UUUCAGGC@LB@ \|\|\| \|\|\|\|\| \|\|:\| :\|: \|\| \|\|\|\|\|\|\|\|@LB@ UCA UGUUC CCGU UCG AC AAAGUCCG@LB@3'-UUU...ACUAC A G UG AA GCGUG-5'@LB@ \| \|@LB@ 37 5@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -27.3223 kcal/mol@LB@Unfolding Energy - mRNA 5.11839 kcal/mol@LB@Unfolding Energy - sRNA 11.9979 kcal/mol@LB@@LB@Position - mRNA 180 -- 212@LB@Position - sRNA 6 -- 36@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 6 -- 12@LB@
100	0.00547	0.1855	b2451	eutA	-10.77	0.099200	8 -- 32	56 -- 86	reactivating factor for ethanolamine ammonia lyase		_____________7_______________________________33\n_____________\|_______________________________\|\n____5'-GUCAUCA________UU______________CC_____UUUCG...UGU-3'\n______________ACUGCGCC__CGCC______GUUU__GCUGC\n______________\|\|\|\|\|\|\|\|__\|:\|\|______:\|:\|__\|\|\|\|\|\n______________UGACGCGG__GUGG______UAGA__CGACG\n3'-UUU...GCUUA________UU____UCCCUU____AC_____CGGCA...GUG-5'\n_____________\|_______________________________\|\n_____________87______________________________55\n	9 -- 15	79 -- 85	-30.9169 kcal/mol	5.09004 kcal/mol	15.0537 kcal/mol	7 33@LB@ \| \|@LB@ 5'-GUCAUCA UU CC UUUCG...UGU-3'@LB@ ACUGCGCC CGCC GUUU GCUGC@LB@ \|\|\|\|\|\|\|\| \|:\|\| :\|:\| \|\|\|\|\|@LB@ UGACGCGG GUGG UAGA CGACG@LB@3'-UUU...GCUUA UU UCCCUU AC CGGCA...GUG-5'@LB@ \| \|@LB@ 87 55@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -30.9169 kcal/mol@LB@Unfolding Energy - mRNA 5.09004 kcal/mol@LB@Unfolding Energy - sRNA 15.0537 kcal/mol@LB@@LB@Position - mRNA 8 -- 32@LB@Position - sRNA 56 -- 86@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 79 -- 85@LB@
193	0.01192	0.2159	b2453	eutG	-10.04	0.136932	27 -- 40	17 -- 30	ethanol dehydrogenase involved in ethanolamine utilization; aldehyde reductase		_____________26_____________41\n_____________\|______________\|\n5'-GGC...UAUUG_______G______ACUGA...GUC-3'\n______________AAGGGCA_GGCAUU\n______________\|\|\|\|\|\|\|_:\|\|\|:\|\n______________UUCCCGU_UCGUGA\n3'-UUU...CAAUG_______G______CAAAA...GUG-5'\n_____________\|______________\|\n_____________31_____________16\n	27 -- 33	24 -- 30	-21.9245 kcal/mol	3.17394 kcal/mol	8.71417 kcal/mol	26 41@LB@ \| \|@LB@5'-GGC...UAUUG G ACUGA...GUC-3'@LB@ AAGGGCA GGCAUU@LB@ \|\|\|\|\|\|\| :\|\|\|:\|@LB@ UUCCCGU UCGUGA@LB@3'-UUU...CAAUG G CAAAA...GUG-5'@LB@ \| \|@LB@ 31 16@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -21.9245 kcal/mol@LB@Unfolding Energy - mRNA 3.17394 kcal/mol@LB@Unfolding Energy - sRNA 8.71417 kcal/mol@LB@@LB@Position - mRNA 27 -- 40@LB@Position - sRNA 17 -- 30@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 24 -- 30@LB@
19	0.001118	0.1727	b2455	eutE	-12.39	0.048028	37 -- 59	68 -- 89	aldehyde oxidoreductase ethanolamine utilization protein		_____________36______________________60\n_____________\|_______________________\|\n5'-GGU...UCGAC_______G___G__A________GUGGG...UCG-3'\n______________AAUAUUG_CGC_GG_ACCGGGGA\n______________\|\|\|\|:\|\|_\|\|\|_::_\|\|\|:\|\|\|\|\n______________UUAUGAC_GCG_UU_UGGUCCCU\n3'-UUU...CGCGC___________G__G________UUAGA...GUG-5'\n_____________\|_______________________\|\n_____________90______________________67\n	37 -- 43	83 -- 89	-25.7412 kcal/mol	5.46666 kcal/mol	7.88032 kcal/mol	36 60@LB@ \| \|@LB@5'-GGU...UCGAC G G A GUGGG...UCG-3'@LB@ AAUAUUG CGC GG ACCGGGGA@LB@ \|\|\|\|:\|\| \|\|\| :: \|\|\|:\|\|\|\|@LB@ UUAUGAC GCG UU UGGUCCCU@LB@3'-UUU...CGCGC G G UUAGA...GUG-5'@LB@ \| \|@LB@ 90 67@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -25.7412 kcal/mol@LB@Unfolding Energy - mRNA 5.46666 kcal/mol@LB@Unfolding Energy - sRNA 7.88032 kcal/mol@LB@@LB@Position - mRNA 37 -- 59@LB@Position - sRNA 68 -- 89@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 83 -- 89@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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