Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
151	0.0157	0.3349	b0586	entF	-8.26	0.051334	189 -- 199	37 -- 47	enterobactin synthase multienzyme complex component ATP-dependent	_____________188_________200\n_____________\|___________\|\n5'-CCC...CAGUU___________AAUGA...UUG-3'\n______________GCAGGAGGCAC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CGUUCUUCGUG\n3'-UUU...GAAUU___________AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	193 -- 199	37 -- 43	-17.6877 kcal/mol	4.1913 kcal/mol	5.23944 kcal/mol	188 200@LB@ \| \|@LB@5'-CCC...CAGUU AAUGA...UUG-3'@LB@ GCAGGAGGCAC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CGUUCUUCGUG@LB@3'-UUU...GAAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -17.6877 kcal/mol@LB@Unfolding Energy - mRNA 4.1913 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 189 -- 199@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 37 -- 43@LB@
152	0.01589	0.3359	b3428	glgP	-3.42	0.610648	252 -- 258	36 -- 42	glycogen phosphorylase	_____________251_____259\n_____________\|_______\|\n5'-CCA...CUCUU_______CUAUC...CGG-3'\n______________AAGCACU\n______________\|\|\|\|\|\|\|\n______________UUCGUGA\n3'-UUU...CGUUC_______AUUUU...CAA-5'\n_____________\|_______\|\n_____________43______35\n	252 -- 258	36 -- 42	-8.34293 kcal/mol	3.32239 kcal/mol	1.60154 kcal/mol	251 259@LB@ \| \|@LB@5'-CCA...CUCUU CUAUC...CGG-3'@LB@ AAGCACU@LB@ \|\|\|\|\|\|\|@LB@ UUCGUGA@LB@3'-UUU...CGUUC AUUUU...CAA-5'@LB@ \| \|@LB@ 43 35@LB@@LB@@LB@Energy -3.42 kcal/mol@LB@Hybridization Energy -8.34293 kcal/mol@LB@Unfolding Energy - mRNA 3.32239 kcal/mol@LB@Unfolding Energy - sRNA 1.60154 kcal/mol@LB@@LB@Position - mRNA 252 -- 258@LB@Position - sRNA 36 -- 42@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 36 -- 42@LB@
153	0.016	0.3359	b2167	fruA	-4.10	0.476180	191 -- 199	37 -- 45	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________190_______200\n_____________\|_________\|\n5'-CGC...AGCAG_________AAUGA...AAA-3'\n______________GAGAGGCAU\n______________:\|\|\|:\|\|\|:\n______________UUCUUCGUG\n3'-UUU...AUUCG_________AAUUU...CAA-5'\n_____________\|_________\|\n_____________46________36\n	193 -- 199	37 -- 43	-10.9543 kcal/mol	1.97714 kcal/mol	4.8783 kcal/mol	190 200@LB@ \| \|@LB@5'-CGC...AGCAG AAUGA...AAA-3'@LB@ GAGAGGCAU@LB@ :\|\|\|:\|\|\|:@LB@ UUCUUCGUG@LB@3'-UUU...AUUCG AAUUU...CAA-5'@LB@ \| \|@LB@ 46 36@LB@@LB@@LB@Energy -4.10 kcal/mol@LB@Hybridization Energy -10.9543 kcal/mol@LB@Unfolding Energy - mRNA 1.97714 kcal/mol@LB@Unfolding Energy - sRNA 4.8783 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 37 -- 45@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 37 -- 43@LB@
154	0.01606	0.3359	b2587	kgtP	-4.55	0.394910	6 -- 12	52 -- 58	alpha-ketoglutarate transporter	_____________5_______13\n_____________\|_______\|\n______5'-UCCCC_______CCACU...UCG-3'\n______________AACUUGC\n______________\|\|\|\|\|\|\|\n______________UUGAACG\n3'-UUU...CUACU_______AAUUC...CAA-5'\n_____________\|_______\|\n_____________59______51\n	6 -- 12	52 -- 58	-7.82918 kcal/mol	0.15004 kcal/mol	3.13411 kcal/mol	5 13@LB@ \| \|@LB@ 5'-UCCCC CCACU...UCG-3'@LB@ AACUUGC@LB@ \|\|\|\|\|\|\|@LB@ UUGAACG@LB@3'-UUU...CUACU AAUUC...CAA-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -4.55 kcal/mol@LB@Hybridization Energy -7.82918 kcal/mol@LB@Unfolding Energy - mRNA 0.15004 kcal/mol@LB@Unfolding Energy - sRNA 3.13411 kcal/mol@LB@@LB@Position - mRNA 6 -- 12@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 52 -- 58@LB@
155	0.01672	0.3455	b1686	menI	-4.77	0.356790	227 -- 235	36 -- 44	1 4-dihydroxy-2-naphthoyl-CoA hydrolase	_____________226_______236\n_____________\|_________\|\n5'-GGC...ACCCU_________GAAUG...AUG-3'\n______________GGAAGCACU\n______________:\|\|\|\|\|\|\|\|\n______________UCUUCGUGA\n3'-UUU...UUCGU_________AUUUU...CAA-5'\n_____________\|_________\|\n_____________45________35\n	229 -- 235	36 -- 42	-13.4239 kcal/mol	4.1512 kcal/mol	4.5009 kcal/mol	226 236@LB@ \| \|@LB@5'-GGC...ACCCU GAAUG...AUG-3'@LB@ GGAAGCACU@LB@ :\|\|\|\|\|\|\|\|@LB@ UCUUCGUGA@LB@3'-UUU...UUCGU AUUUU...CAA-5'@LB@ \| \|@LB@ 45 35@LB@@LB@@LB@Energy -4.77 kcal/mol@LB@Hybridization Energy -13.4239 kcal/mol@LB@Unfolding Energy - mRNA 4.1512 kcal/mol@LB@Unfolding Energy - sRNA 4.5009 kcal/mol@LB@@LB@Position - mRNA 227 -- 235@LB@Position - sRNA 36 -- 44@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 36 -- 42@LB@
156	0.01673	0.3455	b0740	tolB	-6.75	0.127692	202 -- 229	33 -- 61	periplasmic protein	_____________201____________________________230\n_____________\|______________________________\|\n5'-UCC...UAUGA______AG__A_________U_________UUUUC...CCG-3'\n______________UGAAGC__GC_UUA__CGAG_AGCAUUUGG\n______________\|\|\|\|:\|__\|\|_\|\|\|__\|:\|\|_\|\|\|\|:\|\|::\n______________ACUUUG__CG_AAU__GUUC_UCGUGAAUU\n3'-UUU...GCCCU______AA______UC____U_________UUUUA...CAA-5'\n_____________\|______________________________\|\n_____________62_____________________________32\n	222 -- 228	34 -- 40	-20.0945 kcal/mol	5.97693 kcal/mol	7.37029 kcal/mol	201 230@LB@ \| \|@LB@5'-UCC...UAUGA AG A U UUUUC...CCG-3'@LB@ UGAAGC GC UUA CGAG AGCAUUUGG@LB@ \|\|\|\|:\| \|\| \|\|\| \|:\|\| \|\|\|\|:\|\|::@LB@ ACUUUG CG AAU GUUC UCGUGAAUU@LB@3'-UUU...GCCCU AA UC U UUUUA...CAA-5'@LB@ \| \|@LB@ 62 32@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -20.0945 kcal/mol@LB@Unfolding Energy - mRNA 5.97693 kcal/mol@LB@Unfolding Energy - sRNA 7.37029 kcal/mol@LB@@LB@Position - mRNA 202 -- 229@LB@Position - sRNA 33 -- 61@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 34 -- 40@LB@
157	0.01701	0.3489	b3856	mobB	-4.94	0.329991	189 -- 197	52 -- 60	molybdopterin-guanine dinucleotide biosynthesis protein B	_____________188_______198\n_____________\|_________\|\n5'-GUG...CCAGA_________CCGAU...CCA-3'\n______________GGAGCUUGC\n______________\|:\|:\|\|\|\|\|\n______________CUUUGAACG\n3'-UUU...CCCUA_________AAUUC...CAA-5'\n_____________\|_________\|\n_____________61________51\n	191 -- 197	52 -- 58	-10.6989 kcal/mol	2.59286 kcal/mol	3.16562 kcal/mol	188 198@LB@ \| \|@LB@5'-GUG...CCAGA CCGAU...CCA-3'@LB@ GGAGCUUGC@LB@ \|:\|:\|\|\|\|\|@LB@ CUUUGAACG@LB@3'-UUU...CCCUA AAUUC...CAA-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -4.94 kcal/mol@LB@Hybridization Energy -10.6989 kcal/mol@LB@Unfolding Energy - mRNA 2.59286 kcal/mol@LB@Unfolding Energy - sRNA 3.16562 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 52 -- 58@LB@
158	0.01725	0.3504	b3857	mobA	-11.09	0.007545	184 -- 212	5 -- 35	molybdopterin-guanine dinucleotide synthase	_____________183_____________________________213\n_____________\|_______________________________\|\n5'-UCC...CACAA_______GG___________U__________ACGAC...AAC-3'\n______________UAAAAGA__CG__AUAUCGG_GAAUCUGAUG\n______________\|\|\|\|\|:\|__\|\|__\|:\|:\|:\|_:\|\|\|\|\|\|\|\|\|\n______________AUUUUUU__GC__UGUGGUC_UUUAGACUAC\n3'-UUU...CGUGA_______AA__AA_______C__________ACAA-5'\n_____________\|_______________________________\|\n_____________36______________________________4\n	184 -- 190	29 -- 35	-25.0811 kcal/mol	5.24608 kcal/mol	8.74745 kcal/mol	183 213@LB@ \| \|@LB@5'-UCC...CACAA GG U ACGAC...AAC-3'@LB@ UAAAAGA CG AUAUCGG GAAUCUGAUG@LB@ \|\|\|\|\|:\| \|\| \|:\|:\|:\| :\|\|\|\|\|\|\|\|\|@LB@ AUUUUUU GC UGUGGUC UUUAGACUAC@LB@3'-UUU...CGUGA AA AA C ACAA-5'@LB@ \| \|@LB@ 36 4@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -25.0811 kcal/mol@LB@Unfolding Energy - mRNA 5.24608 kcal/mol@LB@Unfolding Energy - sRNA 8.74745 kcal/mol@LB@@LB@Position - mRNA 184 -- 212@LB@Position - sRNA 5 -- 35@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 29 -- 35@LB@
159	0.01739	0.3504	b2426	ucpA	-8.50	0.043854	215 -- 229	36 -- 49	furfural resistance protein putative short-chain oxidoreductase	_____________214_____________230\n_____________\|_______________\|\n5'-GUG...CUCAC________C______GAUUA...UAA-3'\n______________GGGCAAGA_AGCACU\n______________::\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UUCGUUCU_UCGUGA\n3'-UUU...ACGAA_______________AUUUU...CAA-5'\n_____________\|_______________\|\n_____________50______________35\n	216 -- 222	42 -- 48	-19.0239 kcal/mol	4.4828 kcal/mol	6.03645 kcal/mol	214 230@LB@ \| \|@LB@5'-GUG...CUCAC C GAUUA...UAA-3'@LB@ GGGCAAGA AGCACU@LB@ ::\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUCGUUCU UCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -19.0239 kcal/mol@LB@Unfolding Energy - mRNA 4.4828 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 215 -- 229@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 42 -- 48@LB@
160	0.01746	0.3504	b4542	yohO	-11.65	0.004993	133 -- 150	23 -- 41	putative membrane protein	_____________132_________________151\n_____________\|___________________\|\n5'-UCG...CACUC_________U_________AACAA...GUG-3'\n______________GGCAUUUAA__GAUUCGUU\n______________:\|\|\|:\|\|\|\|__:\|\|\|\|\|\|\|\n______________UCGUGAAUU__UUAAGCAA\n3'-UUU...GUUCU_________UU________UGUGG...CAA-5'\n_____________\|___________________\|\n_____________42__________________22\n	144 -- 150	23 -- 29	-16.4387 kcal/mol	3.13759 kcal/mol	1.64896 kcal/mol	132 151@LB@ \| \|@LB@5'-UCG...CACUC U AACAA...GUG-3'@LB@ GGCAUUUAA GAUUCGUU@LB@ :\|\|\|:\|\|\|\| :\|\|\|\|\|\|\|@LB@ UCGUGAAUU UUAAGCAA@LB@3'-UUU...GUUCU UU UGUGG...CAA-5'@LB@ \| \|@LB@ 42 22@LB@@LB@@LB@Energy -11.65 kcal/mol@LB@Hybridization Energy -16.4387 kcal/mol@LB@Unfolding Energy - mRNA 3.13759 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 133 -- 150@LB@Position - sRNA 23 -- 41@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 23 -- 29@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)

Job resubmission

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service.

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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