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
141	0.008132	0.2031	b3412	bioH	-10.51	0.111302	230 -- 255	56 -- 74	pimeloyl-ACP methyl ester carboxylesterase	_____________229________________________256\n_____________\|__________________________\|\n5'-GGC...AAAGG________AUGUUC______U_____UGCAC...ACG-3'\n______________UCAGGGGA______AUCUUG_GCUGC\n______________:\|\|\|\|\|:\|______\|\|\|\|\|\|_\|\|\|\|\|\n______________GGUCCCUU______UAGAAC_CGACG\n3'-UUU...GUUGU__________________________CGGCA...GUG-5'\n_____________\|__________________________\|\n_____________75_________________________55\n	231 -- 237	67 -- 73	-25.2186 kcal/mol	6.56983 kcal/mol	8.13729 kcal/mol	229 256@LB@ \| \|@LB@5'-GGC...AAAGG AUGUUC U UGCAC...ACG-3'@LB@ UCAGGGGA AUCUUG GCUGC@LB@ :\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\|\|@LB@ GGUCCCUU UAGAAC CGACG@LB@3'-UUU...GUUGU CGGCA...GUG-5'@LB@ \| \|@LB@ 75 55@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -25.2186 kcal/mol@LB@Unfolding Energy - mRNA 6.56983 kcal/mol@LB@Unfolding Energy - sRNA 8.13729 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 56 -- 74@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 67 -- 73@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@
124	0.006738	0.1913	b2533	suhB	-10.44	0.114821	158 -- 166	51 -- 59	inositol monophosphatase	_____________157_______167\n_____________\|_________\|\n5'-UUG...AUACU_________UUUCC...AGA-3'\n______________CUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\n______________GACGCGGCA\n3'-UUU...GAACC_________UUUAA...GUG-5'\n_____________\|_________\|\n_____________60________50\n	160 -- 166	51 -- 57	-17.2912 kcal/mol	2.02049 kcal/mol	4.83013 kcal/mol	157 167@LB@ \| \|@LB@5'-UUG...AUACU UUUCC...AGA-3'@LB@ CUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|@LB@ GACGCGGCA@LB@3'-UUU...GAACC UUUAA...GUG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -17.2912 kcal/mol@LB@Unfolding Energy - mRNA 2.02049 kcal/mol@LB@Unfolding Energy - sRNA 4.83013 kcal/mol@LB@@LB@Position - mRNA 158 -- 166@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 51 -- 57@LB@
98	0.005208	0.1855	b4174	hflK	-10.42	0.116019	265 -- 284	65 -- 83	modulator for HflB protease specific for phage lambda cII repressor	_____________264__________________285\n_____________\|____________________\|\n5'-AGA...ACCUG___G____U__G________GGAAA...GUC-3'\n______________GCG_CAAC_CU_AGGGAAAU\n______________\|\|\|_\|\|\|\|_\|:_\|\|\|\|\|\|\|\|\n______________CGC_GUUG_GG_UCCCUUUA\n3'-UUU...UAUGA___G____U___________GAACC...GUG-5'\n_____________\|____________________\|\n_____________84___________________64\n	278 -- 284	65 -- 71	-24.0318 kcal/mol	6.25533 kcal/mol	7.35968 kcal/mol	264 285@LB@ \| \|@LB@5'-AGA...ACCUG G U G GGAAA...GUC-3'@LB@ GCG CAAC CU AGGGAAAU@LB@ \|\|\| \|\|\|\| \|: \|\|\|\|\|\|\|\|@LB@ CGC GUUG GG UCCCUUUA@LB@3'-UUU...UAUGA G U GAACC...GUG-5'@LB@ \| \|@LB@ 84 64@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -24.0318 kcal/mol@LB@Unfolding Energy - mRNA 6.25533 kcal/mol@LB@Unfolding Energy - sRNA 7.35968 kcal/mol@LB@@LB@Position - mRNA 265 -- 284@LB@Position - sRNA 65 -- 83@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 65 -- 71@LB@
171	0.01011	0.2071	b4086	alsC	-10.38	0.118114	189 -- 207	53 -- 70	D-allose ABC transporter permease	_____________188_________________208\n_____________\|___________________\|\n5'-CGC...GAAGA_______A____A__G___UUACC...CGA-3'\n______________GGAGAUU_UGGC_UG_GCU\n______________\|\|\|:\|\|:_\|\|\|\|_\|\|_\|\|:\n______________CCUUUAG_ACCG_AC_CGG\n3'-UUU...UGGUC_______A_______G___CAUUU...GUG-5'\n_____________\|___________________\|\n_____________71__________________52\n	189 -- 195	64 -- 70	-21.9341 kcal/mol	4.72392 kcal/mol	6.83419 kcal/mol	188 208@LB@ \| \|@LB@5'-CGC...GAAGA A A G UUACC...CGA-3'@LB@ GGAGAUU UGGC UG GCU@LB@ \|\|\|:\|\|: \|\|\|\| \|\| \|\|:@LB@ CCUUUAG ACCG AC CGG@LB@3'-UUU...UGGUC A G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -21.9341 kcal/mol@LB@Unfolding Energy - mRNA 4.72392 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 64 -- 70@LB@
78	0.004296	0.1855	b3258	panF	-10.37	0.118507	142 -- 153	52 -- 62	pantothenate:sodium symporter	_____________141__________154\n_____________\|____________\|\n5'-GGC...UUUAU___A________GGCGA...UUA-3'\n______________UGG_CUGUGCUG\n______________\|\|\|_\|\|\|:\|\|:\|\n______________ACC_GACGCGGC\n3'-UUU...UUAGA____________AUUUA...GUG-5'\n_____________\|____________\|\n_____________63___________51\n	147 -- 153	52 -- 58	-17.1407 kcal/mol	1.89201 kcal/mol	4.8804 kcal/mol	141 154@LB@ \| \|@LB@5'-GGC...UUUAU A GGCGA...UUA-3'@LB@ UGG CUGUGCUG@LB@ \|\|\| \|\|\|:\|\|:\|@LB@ ACC GACGCGGC@LB@3'-UUU...UUAGA AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -17.1407 kcal/mol@LB@Unfolding Energy - mRNA 1.89201 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 52 -- 58@LB@
113	0.005997	0.1855	b1765	ydjA	-10.36	0.119141	118 -- 144	49 -- 76	putative oxidoreductase	_____________117___________________________145\n_____________\|_____________________________\|\n5'-AUU...CUUGU__G__________GC__A___________CAAAA...GUA-3'\n______________CA_CAGG__AAUU__GG_CUGUGCUGUAA\n______________\|\|_\|\|\|\|__\|\|\|:__\|\|_\|\|\|:\|\|:\|\|\|\|\n______________GU_GUCC__UUAG__CC_GACGCGGCAUU\n3'-UUU...CGGUU__G____CU____AA______________UAAUA...GUG-5'\n_____________\|_____________________________\|\n_____________77____________________________48\n	138 -- 144	49 -- 55	-28.7704 kcal/mol	9.07167 kcal/mol	9.34253 kcal/mol	117 145@LB@ \| \|@LB@5'-AUU...CUUGU G GC A CAAAA...GUA-3'@LB@ CA CAGG AAUU GG CUGUGCUGUAA@LB@ \|\| \|\|\|\| \|\|\|: \|\| \|\|\|:\|\|:\|\|\|\|@LB@ GU GUCC UUAG CC GACGCGGCAUU@LB@3'-UUU...CGGUU G CU AA UAAUA...GUG-5'@LB@ \| \|@LB@ 77 48@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -28.7704 kcal/mol@LB@Unfolding Energy - mRNA 9.07167 kcal/mol@LB@Unfolding Energy - sRNA 9.34253 kcal/mol@LB@@LB@Position - mRNA 118 -- 144@LB@Position - sRNA 49 -- 76@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 49 -- 55@LB@
175	0.01031	0.2074	b1834	yebT	-10.32	0.121003	270 -- 282	51 -- 62	MCE domain protein	_____________269___________283\n_____________\|_____________\|\n5'-UCU...CUUUC_______U_____UCAUC...UUG-3'\n______________UGGCUGC_GCCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\n______________ACCGACG_CGGCA\n3'-UUU...UUAGA_____________UUUAA...GUG-5'\n_____________\|_____________\|\n_____________63____________50\n	270 -- 276	56 -- 62	-21.4836 kcal/mol	6.28034 kcal/mol	4.8826 kcal/mol	269 283@LB@ \| \|@LB@5'-UCU...CUUUC U UCAUC...UUG-3'@LB@ UGGCUGC GCCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|@LB@ ACCGACG CGGCA@LB@3'-UUU...UUAGA UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -21.4836 kcal/mol@LB@Unfolding Energy - mRNA 6.28034 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 270 -- 282@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 56 -- 62@LB@
67	0.003373	0.1727	b0723	sdhA	-10.29	0.122560	175 -- 204	36 -- 70	succinate dehydrogenase flavoprotein subunit	_____________174_________________________________205\n_____________\|___________________________________\|\n5'-GGU...UUUAU___U____________G______GUG_________AAUUG...GUG-3'\n______________GGA__UC___GUUGUG_UGUGGG____UGUGAUGA\n______________\|\|\|__\|\|___\|:\|\|:\|_:\|\|:::____\|:\|\|\|\|\|\|\n______________CCU__AG___CGACGC_GCAUUU____AUACUACU\n3'-UUU...UGGUC___UU__AAC______G______AAUA________CAAUG...GUG-5'\n_____________\|___________________________________\|\n_____________71__________________________________35\n	198 -- 204	36 -- 42	-24.7755 kcal/mol	5.81881 kcal/mol	8.66537 kcal/mol	174 205@LB@ \| \|@LB@5'-GGU...UUUAU U G GUG AAUUG...GUG-3'@LB@ GGA UC GUUGUG UGUGGG UGUGAUGA@LB@ \|\|\| \|\| \|:\|\|:\| :\|\|::: \|:\|\|\|\|\|\|@LB@ CCU AG CGACGC GCAUUU AUACUACU@LB@3'-UUU...UGGUC UU AAC G AAUA CAAUG...GUG-5'@LB@ \| \|@LB@ 71 35@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -24.7755 kcal/mol@LB@Unfolding Energy - mRNA 5.81881 kcal/mol@LB@Unfolding Energy - sRNA 8.66537 kcal/mol@LB@@LB@Position - mRNA 175 -- 204@LB@Position - sRNA 36 -- 70@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 36 -- 42@LB@
122	0.006658	0.1913	b0600	ybdL	-10.23	0.125775	275 -- 297	68 -- 86	methionine aminotransferase PLP-dependent	_____________274_____________________298\n_____________\|_______________________\|\n5'-UCA...AGCGC___G____AG__________C__UUA-3'\n______________GCU_GCGC__CAACACCAGG_GA\n______________:\|\|_\|\|\|\|__\|\|\|\|\|\|\|\|\|\|_\|\|\n______________UGA_CGCG__GUUGUGGUCC_CU\n3'-UUU...GCUUA_______________________UUAGA...GUG-5'\n_____________\|_______________________\|\n_____________87______________________67\n	288 -- 294	70 -- 76	-27.7616 kcal/mol	10.1544 kcal/mol	7.37523 kcal/mol	274 298@LB@ \| \|@LB@5'-UCA...AGCGC G AG C UUA-3'@LB@ GCU GCGC CAACACCAGG GA@LB@ :\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UGA CGCG GUUGUGGUCC CU@LB@3'-UUU...GCUUA UUAGA...GUG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -27.7616 kcal/mol@LB@Unfolding Energy - mRNA 10.1544 kcal/mol@LB@Unfolding Energy - sRNA 7.37523 kcal/mol@LB@@LB@Position - mRNA 275 -- 297@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 70 -- 76@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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