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
32	0.0005297	0.05563	b3456	livM	-14.95	0.011565	245 -- 274	15 -- 42	branched-chain amino acid ABC transporter permease	_____________244____________________________275\n_____________\|______________________________\|\n5'-GCC...GCGAU______U____U___G_____C________CGUGC...CCA-3'\n______________GUUCUU_GUGC_GGC_GGCGU_UUUAUGGG\n______________\|\|\|\|:\|_\|\|:\|_:\|\|_:\|\|:\|_\|\|\|\|\|\|\|\|\n______________CAAGGA_CAUG_UCG_UCGUA_AAAUACCC\n3'-UUU...UCCAC______C________A______________AAUAC...UCG-5'\n_____________\|______________________________\|\n_____________43_____________________________14\n	268 -- 274	15 -- 21	-29.6256 kcal/mol	10.1077 kcal/mol	4.57031 kcal/mol	244 275@LB@ \| \|@LB@5'-GCC...GCGAU U U G C CGUGC...CCA-3'@LB@ GUUCUU GUGC GGC GGCGU UUUAUGGG@LB@ \|\|\|\|:\| \|\|:\| :\|\| :\|\|:\| \|\|\|\|\|\|\|\|@LB@ CAAGGA CAUG UCG UCGUA AAAUACCC@LB@3'-UUU...UCCAC C A AAUAC...UCG-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -14.95 kcal/mol@LB@Hybridization Energy -29.6256 kcal/mol@LB@Unfolding Energy - mRNA 10.1077 kcal/mol@LB@Unfolding Energy - sRNA 4.57031 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 15 -- 21@LB@
194	0.01107	0.1919	b3288	fmt	-14.89	0.012048	76 -- 114	11 -- 48	10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase	_____________75_______________________________________115\n_____________\|________________________________________\|\n5'-AUU...AGCAU___A___AUCA___________AAACUG_______A____CUGUC...UGU-3'\n______________GAG_UGG____CCUGGU_CGGC______UUUAUGG_UUAU\n______________\|\|\|_\|\|\|____\|\|\|\|\|\|_\|:\|\|______\|\|\|\|\|\|\|_\|\|\|\|\n______________CUC_ACC____GGACCA_GUCG______AAAUACC_AAUA\n3'-UUU...GAUUC___C___AA________U____AUCGUA_______C____CAAAA...UCG-5'\n_____________\|________________________________________\|\n_____________49_______________________________________10\n	103 -- 109	16 -- 22	-29.2084 kcal/mol	9.72928 kcal/mol	4.59227 kcal/mol	75 115@LB@ \| \|@LB@5'-AUU...AGCAU A AUCA AAACUG A CUGUC...UGU-3'@LB@ GAG UGG CCUGGU CGGC UUUAUGG UUAU@LB@ \|\|\| \|\|\| \|\|\|\|\|\| \|:\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ CUC ACC GGACCA GUCG AAAUACC AAUA@LB@3'-UUU...GAUUC C AA U AUCGUA C CAAAA...UCG-5'@LB@ \| \|@LB@ 49 10@LB@@LB@@LB@Energy -14.89 kcal/mol@LB@Hybridization Energy -29.2084 kcal/mol@LB@Unfolding Energy - mRNA 9.72928 kcal/mol@LB@Unfolding Energy - sRNA 4.59227 kcal/mol@LB@@LB@Position - mRNA 76 -- 114@LB@Position - sRNA 11 -- 48@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 16 -- 22@LB@
148	0.00721	0.1633	b0643	ybeL	-14.84	0.012433	12 -- 39	23 -- 48	DUF1451 family protein	_____________11___________________________40\n_____________\|____________________________\|\n5'-AAU...GCGUU____________CAGAU_C__A______AGCCC...CGC-3'\n______________GAGGUGGUUUUU_____C_GC_UAGCAU\n______________\|\|\|\|\|\|\|\|\|::\|_____\|_\|\|_\|\|\|\|\|\|\n______________CUCCACCAAGGA_____G_CG_AUCGUA\n3'-UUU...GAUUC____________CCAU__U_________AAAUA...UCG-5'\n_____________\|____________________________\|\n_____________49___________________________22\n	17 -- 23	37 -- 43	-25.8201 kcal/mol	6.42089 kcal/mol	4.55935 kcal/mol	11 40@LB@ \| \|@LB@5'-AAU...GCGUU CAGAU C A AGCCC...CGC-3'@LB@ GAGGUGGUUUUU C GC UAGCAU@LB@ \|\|\|\|\|\|\|\|\|::\| \| \|\| \|\|\|\|\|\|@LB@ CUCCACCAAGGA G CG AUCGUA@LB@3'-UUU...GAUUC CCAU U AAAUA...UCG-5'@LB@ \| \|@LB@ 49 22@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -25.8201 kcal/mol@LB@Unfolding Energy - mRNA 6.42089 kcal/mol@LB@Unfolding Energy - sRNA 4.55935 kcal/mol@LB@@LB@Position - mRNA 12 -- 39@LB@Position - sRNA 23 -- 48@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 37 -- 43@LB@
52	0.001222	0.07744	b2217	rcsB	-14.74	0.013297	68 -- 91	9 -- 38	response regulator in two-component regulatory system with RcsC and YojN	_____________67_______________________________92\n_____________\|________________________________\|\n5'-AAC...UAAAU_______CC___A___________________GAAAC...GCG-3'\n______________CUGGUAC__GGC_AGCA________GUUAUGU\n______________\|\|\|\|\|\|\|__:\|\|_\|\|\|\|________\|\|\|\|\|\|\|\n______________GACCAUG__UCG_UCGU________CAAUACA\n3'-UUU...CCAAG____________A____AAAAUACC_______AAAAGUCG-5'\n_____________\|________________________________\|\n_____________39_______________________________8\n	85 -- 91	9 -- 15	-24.0406 kcal/mol	4.76673 kcal/mol	4.53501 kcal/mol	67 92@LB@ \| \|@LB@5'-AAC...UAAAU CC A GAAAC...GCG-3'@LB@ CUGGUAC GGC AGCA GUUAUGU@LB@ \|\|\|\|\|\|\| :\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ GACCAUG UCG UCGU CAAUACA@LB@3'-UUU...CCAAG A AAAAUACC AAAAGUCG-5'@LB@ \| \|@LB@ 39 8@LB@@LB@@LB@Energy -14.74 kcal/mol@LB@Hybridization Energy -24.0406 kcal/mol@LB@Unfolding Energy - mRNA 4.76673 kcal/mol@LB@Unfolding Energy - sRNA 4.53501 kcal/mol@LB@@LB@Position - mRNA 68 -- 91@LB@Position - sRNA 9 -- 38@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 9 -- 15@LB@
4	1.432e-06	0.001203	b4547	ypfN	-14.60	0.014593	223 -- 236	33 -- 46	putative membrane protein UPF0370 family	_____________222____________237\n_____________\|______________\|\n5'-UGA...AUAUU_____A________AUUGU...AGA-3'\n______________GGUGG_UUCUGGUG\n______________\|\|\|\|\|_\|:\|\|\|\|\|:\n______________CCACC_AGGACCAU\n3'-UUU...UUCCU_____A________GUCGA...UCG-5'\n_____________\|______________\|\n_____________47_____________32\n	230 -- 236	33 -- 39	-20.5459 kcal/mol	2.69728 kcal/mol	3.25117 kcal/mol	222 237@LB@ \| \|@LB@5'-UGA...AUAUU A AUUGU...AGA-3'@LB@ GGUGG UUCUGGUG@LB@ \|\|\|\|\| \|:\|\|\|\|\|:@LB@ CCACC AGGACCAU@LB@3'-UUU...UUCCU A GUCGA...UCG-5'@LB@ \| \|@LB@ 47 32@LB@@LB@@LB@Energy -14.60 kcal/mol@LB@Hybridization Energy -20.5459 kcal/mol@LB@Unfolding Energy - mRNA 2.69728 kcal/mol@LB@Unfolding Energy - sRNA 3.25117 kcal/mol@LB@@LB@Position - mRNA 223 -- 236@LB@Position - sRNA 33 -- 46@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 33 -- 39@LB@
145	0.006858	0.158	b2079	baeR	-14.59	0.014658	61 -- 107	1 -- 46	response regulator in two-component regulatory system with BaeS	_____________60________________________________________________108\n_____________\|_________________________________________________\|\n5'-CAG...CCAGC__C______G__C__G________A____CC__AACAU____GA_____ACAUA...CGA-3'\n______________GG_GGUUCC_GG_UG_GGCUGGCG_UUUG__UG_____UGUU____AGC\n______________\|\|_\|\|\|\|\|\|_\|\|_\|:_:\|\|\|:\|\|:_\|\|\|:__\|\|_____\|\|\|\|____\|\|\|\n______________CC_CCAAGG_CC_AU_UCGAUCGU_AAAU__AC_____ACAA____UCG\n3'-UUU...UUCCU__A______A_____G________A________CCAAU____AAAG___-5'\n_____________\|________________________________________________\|\n_____________47_______________________________________________1\n	78 -- 84	24 -- 30	-36.7072 kcal/mol	17.5074 kcal/mol	4.60935 kcal/mol	60 108@LB@ \| \|@LB@5'-CAG...CCAGC C G C G A CC AACAU GA ACAUA...CGA-3'@LB@ GG GGUUCC GG UG GGCUGGCG UUUG UG UGUU AGC@LB@ \|\| \|\|\|\|\|\| \|\| \|: :\|\|\|:\|\|: \|\|\|: \|\| \|\|\|\| \|\|\|@LB@ CC CCAAGG CC AU UCGAUCGU AAAU AC ACAA UCG@LB@3'-UUU...UUCCU A A G A CCAAU AAAG -5'@LB@ \| \|@LB@ 47 1@LB@@LB@@LB@Energy -14.59 kcal/mol@LB@Hybridization Energy -36.7072 kcal/mol@LB@Unfolding Energy - mRNA 17.5074 kcal/mol@LB@Unfolding Energy - sRNA 4.60935 kcal/mol@LB@@LB@Position - mRNA 61 -- 107@LB@Position - sRNA 1 -- 46@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 24 -- 30@LB@
18	0.0001426	0.02662	b1824	yobF	-14.57	0.014857	186 -- 218	1 -- 36	DUF2527 family heat-induced protein	_____________185__________________________________219\n_____________\|____________________________________\|\n5'-GCC...AACGA____________UG______U__GGCA_________AAAGA...UGU-3'\n______________GGUACAGUU__C__UUUAUG_GU_____UUUUCAGU\n______________\|\|\|\|\|\|\|:\|__\|__\|\|\|\|\|\|_\|\|_____\|\|\|\|\|\|\|:\n______________CCAUGUCGA__G__AAAUAC_CA_____AAAAGUCG\n3'-UUU...AAGGA_________UC_UA______C__AUACA________-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	212 -- 218	1 -- 7	-24.9268 kcal/mol	8.86182 kcal/mol	1.49509 kcal/mol	185 219@LB@ \| \|@LB@5'-GCC...AACGA UG U GGCA AAAGA...UGU-3'@LB@ GGUACAGUU C UUUAUG GU UUUUCAGU@LB@ \|\|\|\|\|\|\|:\| \| \|\|\|\|\|\| \|\| \|\|\|\|\|\|\|:@LB@ CCAUGUCGA G AAAUAC CA AAAAGUCG@LB@3'-UUU...AAGGA UC UA C AUACA -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -14.57 kcal/mol@LB@Hybridization Energy -24.9268 kcal/mol@LB@Unfolding Energy - mRNA 8.86182 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 186 -- 218@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 1 -- 7@LB@
185	0.01059	0.1919	b3856	mobB	-14.40	0.016564	123 -- 150	1 -- 31	molybdopterin-guanine dinucleotide biosynthesis protein B	_____________122______________________________151\n_____________\|________________________________\|\n5'-GUG...CGUCU________GUC____C_____A__________GAUCA...CCA-3'\n______________GGCUGGCG____AUG_GGUUG____UUUCAGC\n______________:\|\|\|:\|\|:____\|\|\|_\|\|\|\|:____\|\|\|\|\|\|\|\n______________UCGAUCGU____UAC_CCAAU____AAAGUCG\n3'-UUU...CCAUG________AAAA_________ACAA_______-5'\n_____________\|_______________________________\|\n_____________32______________________________1\n	144 -- 150	1 -- 7	-26.2194 kcal/mol	10.3308 kcal/mol	1.48722 kcal/mol	122 151@LB@ \| \|@LB@5'-GUG...CGUCU GUC C A GAUCA...CCA-3'@LB@ GGCUGGCG AUG GGUUG UUUCAGC@LB@ :\|\|\|:\|\|: \|\|\| \|\|\|\|: \|\|\|\|\|\|\|@LB@ UCGAUCGU UAC CCAAU AAAGUCG@LB@3'-UUU...CCAUG AAAA ACAA -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -14.40 kcal/mol@LB@Hybridization Energy -26.2194 kcal/mol@LB@Unfolding Energy - mRNA 10.3308 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 123 -- 150@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 1 -- 7@LB@
29	0.0004753	0.05348	b3412	bioH	-14.38	0.016792	146 -- 163	23 -- 40	pimeloyl-ACP methyl ester carboxylesterase	_____________145________________164\n_____________\|__________________\|\n5'-GGC...CAUAA___C_____U________AUGUU...ACG-3'\n______________UCC_GGUAC_GUUAGCAU\n______________\|\|\|_\|\|\|\|\|_\|:\|\|\|\|\|\|\n______________AGG_CCAUG_CGAUCGUA\n3'-UUU...CACCA___A_____U________AAAUA...UCG-5'\n_____________\|__________________\|\n_____________41_________________22\n	157 -- 163	23 -- 29	-23.5076 kcal/mol	4.57199 kcal/mol	4.55554 kcal/mol	145 164@LB@ \| \|@LB@5'-GGC...CAUAA C U AUGUU...ACG-3'@LB@ UCC GGUAC GUUAGCAU@LB@ \|\|\| \|\|\|\|\| \|:\|\|\|\|\|\|@LB@ AGG CCAUG CGAUCGUA@LB@3'-UUU...CACCA A U AAAUA...UCG-5'@LB@ \| \|@LB@ 41 22@LB@@LB@@LB@Energy -14.38 kcal/mol@LB@Hybridization Energy -23.5076 kcal/mol@LB@Unfolding Energy - mRNA 4.57199 kcal/mol@LB@Unfolding Energy - sRNA 4.55554 kcal/mol@LB@@LB@Position - mRNA 146 -- 163@LB@Position - sRNA 23 -- 40@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 23 -- 29@LB@
12	4.171e-05	0.01168	b0814	ompX	-14.35	0.017131	192 -- 226	1 -- 48	outer membrane protein X	_____________191______________________________________________227\n_____________\|________________________________________________\|\n5'-CUG...CAUUU_________A___AAAAAAAUU__________________C_______ACUGG...CAC-3'\n______________GAGGUGGUU__UG_________GCA____________UGU_UUUCAGC\n______________\|\|\|\|\|\|\|\|\|__\|\|_________\|\|\|____________\|\|\|_\|\|\|\|\|\|\|\n______________CUCCACCAA__AC_________CGU____________ACA_AAAGUCG\n3'-UUU...GAUUC_________GG__CAUGUCGAU___AAAAUACCCAAU___A_______-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________1\n	220 -- 226	1 -- 7	-27.166 kcal/mol	8.20777 kcal/mol	4.60955 kcal/mol	191 227@LB@ \| \|@LB@5'-CUG...CAUUU A AAAAAAAUU C ACUGG...CAC-3'@LB@ GAGGUGGUU UG GCA UGU UUUCAGC@LB@ \|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CUCCACCAA AC CGU ACA AAAGUCG@LB@3'-UUU...GAUUC GG CAUGUCGAU AAAAUACCCAAU A -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -14.35 kcal/mol@LB@Hybridization Energy -27.166 kcal/mol@LB@Unfolding Energy - mRNA 8.20777 kcal/mol@LB@Unfolding Energy - sRNA 4.60955 kcal/mol@LB@@LB@Position - mRNA 192 -- 226@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 220 -- 226@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)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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