Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
21	0.0001799	0.02879	b0107	hofB	-20.93	0.000028	267 -- 289	25 -- 48	T2SE secretion family protein; P-loop ATPase superfamily protein	_____________266______________________290\n_____________\|________________________\|\n5'-CCA...GCGAA__________A__U__________CGAUG...CUU-3'\n______________GAGGUGGUUC_UG_UGCGG_UAGU\n______________\|\|\|\|\|\|\|\|\|\|_\|\|_\|:\|:\|_\|\|\|:\n______________CUCCACCAAG_AC_AUGUC_AUCG\n3'-UUU...GAUUC__________G__C_____G____UAAAA...UCG-5'\n_____________\|________________________\|\n_____________49_______________________24\n	270 -- 276	39 -- 45	-28.7026 kcal/mol	3.21789 kcal/mol	4.55759 kcal/mol	266 290@LB@ \| \|@LB@5'-CCA...GCGAA A U CGAUG...CUU-3'@LB@ GAGGUGGUUC UG UGCGG UAGU@LB@ \|\|\|\|\|\|\|\|\|\| \|\| \|:\|:\| \|\|\|:@LB@ CUCCACCAAG AC AUGUC AUCG@LB@3'-UUU...GAUUC G C G UAAAA...UCG-5'@LB@ \| \|@LB@ 49 24@LB@@LB@@LB@Energy -20.93 kcal/mol@LB@Hybridization Energy -28.7026 kcal/mol@LB@Unfolding Energy - mRNA 3.21789 kcal/mol@LB@Unfolding Energy - sRNA 4.55759 kcal/mol@LB@@LB@Position - mRNA 267 -- 289@LB@Position - sRNA 25 -- 48@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 39 -- 45@LB@
137	0.006165	0.1512	b1024	pgaA	-6.60	0.530802	267 -- 274	1 -- 8	biofilm adhesin polysaccharide PGA secretin; OM porin; poly-beta-1 6-N-acetyl-D-glucosamine export protein	_____________266______275\n_____________\|________\|\n5'-CUC...CCGCA________AGCGA...CUG-3'\n______________UUUUUAGC\n______________\|\|\|\|:\|\|\|\n______________AAAAGUCG\n3'-UUU...AUACA________-5'\n_____________\|_______\|\n_____________9_______1\n	268 -- 274	1 -- 7	-8.19691 kcal/mol	0.802454 kcal/mol	0.799201 kcal/mol	266 275@LB@ \| \|@LB@5'-CUC...CCGCA AGCGA...CUG-3'@LB@ UUUUUAGC@LB@ \|\|\|\|:\|\|\|@LB@ AAAAGUCG@LB@3'-UUU...AUACA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.60 kcal/mol@LB@Hybridization Energy -8.19691 kcal/mol@LB@Unfolding Energy - mRNA 0.802454 kcal/mol@LB@Unfolding Energy - sRNA 0.799201 kcal/mol@LB@@LB@Position - mRNA 267 -- 274@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 1 -- 7@LB@
172	0.009254	0.1803	b1676	pykF	-8.82	0.265733	268 -- 283	23 -- 40	pyruvate kinase I	_____________267________________284\n_____________\|__________________\|\n5'-GGA...UAAAA_G________________GAACG...UGA-3'\n______________U_CUGG_AC_GCUGGCAU\n______________\|_\|\|\|\|_\|\|_\|\|\|:\|\|\|\|\n______________A_GACC_UG_CGAUCGUA\n3'-UUU...CACCA_G____A__U________AAAUA...UCG-5'\n_____________\|__________________\|\n_____________41_________________22\n	277 -- 283	23 -- 29	-20.12 kcal/mol	6.74388 kcal/mol	4.55554 kcal/mol	267 284@LB@ \| \|@LB@5'-GGA...UAAAA G GAACG...UGA-3'@LB@ U CUGG AC GCUGGCAU@LB@ \| \|\|\|\| \|\| \|\|\|:\|\|\|\|@LB@ A GACC UG CGAUCGUA@LB@3'-UUU...CACCA G A U AAAUA...UCG-5'@LB@ \| \|@LB@ 41 22@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -20.12 kcal/mol@LB@Unfolding Energy - mRNA 6.74388 kcal/mol@LB@Unfolding Energy - sRNA 4.55554 kcal/mol@LB@@LB@Position - mRNA 268 -- 283@LB@Position - sRNA 23 -- 40@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 23 -- 29@LB@
143	0.00681	0.158	b2418	pdxK	-15.34	0.008827	271 -- 292	15 -- 47	pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase	_____________270_______________________________293\n_____________\|_________________________________\|\n5'-CAU...GUCGC_________________________________CAACAGCA-3'\n______________AGGUGGUUU_____ACGGC_AGC_____GUGGG\n______________\|\|\|\|\|\|\|\|:_____\|\|:\|\|_\|\|\|_____:\|\|\|\|\n______________UCCACCAAG_____UGUCG_UCG_____UACCC\n3'-UUU...AUUCC_________GACCA_____A___UAAAA_____AAUAC...UCG-5'\n_____________\|_________________________________\|\n_____________48________________________________14\n	273 -- 279	39 -- 45	-26.4553 kcal/mol	6.54205 kcal/mol	4.57348 kcal/mol	270 293@LB@ \| \|@LB@5'-CAU...GUCGC CAACAGCA-3'@LB@ AGGUGGUUU ACGGC AGC GUGGG@LB@ \|\|\|\|\|\|\|\|: \|\|:\|\| \|\|\| :\|\|\|\|@LB@ UCCACCAAG UGUCG UCG UACCC@LB@3'-UUU...AUUCC GACCA A UAAAA AAUAC...UCG-5'@LB@ \| \|@LB@ 48 14@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -26.4553 kcal/mol@LB@Unfolding Energy - mRNA 6.54205 kcal/mol@LB@Unfolding Energy - sRNA 4.57348 kcal/mol@LB@@LB@Position - mRNA 271 -- 292@LB@Position - sRNA 15 -- 47@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 39 -- 45@LB@
47	0.001093	0.07744	b0128	yadH	-6.67	0.521304	272 -- 286	25 -- 36	putative ABC transporter permease	_____________271_____________287\n_____________\|_______________\|\n5'-UUA...AUCUG_______ACG_____GCCGC...UCA-3'\n______________GGUGCAG___CUGGU\n______________\|\|\|:\|\|\|___\|\|:\|:\n______________CCAUGUC___GAUCG\n3'-UUU...AAGGA_______________UAAAA...UCG-5'\n_____________\|_______________\|\n_____________37______________24\n	272 -- 278	30 -- 36	-13.5693 kcal/mol	5.47586 kcal/mol	1.42738 kcal/mol	271 287@LB@ \| \|@LB@5'-UUA...AUCUG ACG GCCGC...UCA-3'@LB@ GGUGCAG CUGGU@LB@ \|\|\|:\|\|\| \|\|:\|:@LB@ CCAUGUC GAUCG@LB@3'-UUU...AAGGA UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -6.67 kcal/mol@LB@Hybridization Energy -13.5693 kcal/mol@LB@Unfolding Energy - mRNA 5.47586 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 30 -- 36@LB@
30	0.0004774	0.05348	b2148	mglC	-7.69	0.389595	275 -- 281	24 -- 30	methyl-galactoside transporter subunit	_____________274_____282\n_____________\|_______\|\n5'-AUC...GUUUU_______AUUAU...ACC-3'\n______________GCUGGCG\n______________\|\|\|:\|\|:\n______________CGAUCGU\n3'-UUU...CAUGU_______AAAAU...UCG-5'\n_____________\|_______\|\n_____________31______23\n	275 -- 281	24 -- 30	-10.2126 kcal/mol	1.14582 kcal/mol	1.37559 kcal/mol	274 282@LB@ \| \|@LB@5'-AUC...GUUUU AUUAU...ACC-3'@LB@ GCUGGCG@LB@ \|\|\|:\|\|:@LB@ CGAUCGU@LB@3'-UUU...CAUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 31 23@LB@@LB@@LB@Energy -7.69 kcal/mol@LB@Hybridization Energy -10.2126 kcal/mol@LB@Unfolding Energy - mRNA 1.14582 kcal/mol@LB@Unfolding Energy - sRNA 1.37559 kcal/mol@LB@@LB@Position - mRNA 275 -- 281@LB@Position - sRNA 24 -- 30@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 24 -- 30@LB@
120	0.005024	0.1407	b2564	pdxJ	-10.23	0.151404	275 -- 296	21 -- 43	pyridoxine 5'-phosphate synthase	_____________274_____________________297\n_____________\|_______________________\|\n5'-AAA...UACCC__A___________GCC______AUUG-3'\n______________GG_UCC_GGUGCAG___GCGUUU\n______________\|\|_\|\|\|_\|\|\|:\|\|\|___\|\|:\|\|\|\n______________CC_AGG_CCAUGUC___CGUAAA\n3'-UUU...CUCCA__A___A_______GAU______AUACC...UCG-5'\n_____________\|_______________________\|\n_____________44______________________20\n	281 -- 287	30 -- 36	-24.4803 kcal/mol	9.69131 kcal/mol	4.55861 kcal/mol	274 297@LB@ \| \|@LB@5'-AAA...UACCC A GCC AUUG-3'@LB@ GG UCC GGUGCAG GCGUUU@LB@ \|\| \|\|\| \|\|\|:\|\|\| \|\|:\|\|\|@LB@ CC AGG CCAUGUC CGUAAA@LB@3'-UUU...CUCCA A A GAU AUACC...UCG-5'@LB@ \| \|@LB@ 44 20@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -24.4803 kcal/mol@LB@Unfolding Energy - mRNA 9.69131 kcal/mol@LB@Unfolding Energy - sRNA 4.55861 kcal/mol@LB@@LB@Position - mRNA 275 -- 296@LB@Position - sRNA 21 -- 43@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 30 -- 36@LB@
187	0.01074	0.1919	b2536	hcaT	-7.74	0.383266	275 -- 291	25 -- 41	putative 3-phenylpropionic transporter	_____________274_______________292\n_____________\|_________________\|\n5'-UCG...CUACC_______A___U_____UUAAA...GGA-3'\n______________UUUCUGG_GCG_CUGGC\n______________\|\|:\|\|\|\|_:\|:_\|\|:\|\|\n______________AAGGACC_UGU_GAUCG\n3'-UUU...CCACC_______A___C_____UAAAA...UCG-5'\n_____________\|_________________\|\n_____________42________________24\n	275 -- 281	35 -- 41	-17.8602 kcal/mol	5.56231 kcal/mol	4.55428 kcal/mol	274 292@LB@ \| \|@LB@5'-UCG...CUACC A U UUAAA...GGA-3'@LB@ UUUCUGG GCG CUGGC@LB@ \|\|:\|\|\|\| :\|: \|\|:\|\|@LB@ AAGGACC UGU GAUCG@LB@3'-UUU...CCACC A C UAAAA...UCG-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -17.8602 kcal/mol@LB@Unfolding Energy - mRNA 5.56231 kcal/mol@LB@Unfolding Energy - sRNA 4.55428 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 35 -- 41@LB@
33	0.0006117	0.0623	b1795	yeaQ	-12.41	0.053010	276 -- 283	42 -- 49	UPF0410 family protein	_____________275______284\n_____________\|________\|\n5'-AUA...AAGAU________AUUCU...UCC-3'\n______________GGAGGUGG\n______________\|\|\|\|\|\|\|\|\n______________CCUCCACC\n3'-UUU...CGAUU________AAGGA...UCG-5'\n_____________\|________\|\n_____________50_______41\n	277 -- 283	42 -- 48	-16.41 kcal/mol	1.22894 kcal/mol	2.77009 kcal/mol	275 284@LB@ \| \|@LB@5'-AUA...AAGAU AUUCU...UCC-3'@LB@ GGAGGUGG@LB@ \|\|\|\|\|\|\|\|@LB@ CCUCCACC@LB@3'-UUU...CGAUU AAGGA...UCG-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -12.41 kcal/mol@LB@Hybridization Energy -16.41 kcal/mol@LB@Unfolding Energy - mRNA 1.22894 kcal/mol@LB@Unfolding Energy - sRNA 2.77009 kcal/mol@LB@@LB@Position - mRNA 276 -- 283@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 42 -- 48@LB@
49	0.001147	0.07744	b3039	ygiD	-13.27	0.032900	280 -- 298	15 -- 33	4 5- DOPA-extradiol-dioxygenase	_____________279_________________299\n_____________\|___________________\|\n5'-ACG...UACCC__________GAAGU____GA-3'\n______________GCAGCUGGCA_____UGGG\n______________:\|\|\|\|\|:\|\|\|_____\|\|\|\|\n______________UGUCGAUCGU_____ACCC\n3'-UUU...GACCA__________AAAAU____AAUAC...UCG-5'\n_____________\|___________________\|\n_____________34__________________14\n	283 -- 289	24 -- 30	-23.43 kcal/mol	8.71058 kcal/mol	1.44754 kcal/mol	279 299@LB@ \| \|@LB@5'-ACG...UACCC GAAGU GA-3'@LB@ GCAGCUGGCA UGGG@LB@ :\|\|\|\|\|:\|\|\| \|\|\|\|@LB@ UGUCGAUCGU ACCC@LB@3'-UUU...GACCA AAAAU AAUAC...UCG-5'@LB@ \| \|@LB@ 34 14@LB@@LB@@LB@Energy -13.27 kcal/mol@LB@Hybridization Energy -23.43 kcal/mol@LB@Unfolding Energy - mRNA 8.71058 kcal/mol@LB@Unfolding Energy - sRNA 1.44754 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 15 -- 33@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 24 -- 30@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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usability assessment

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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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