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
54	0.002706	0.1597	b0200	gmhB	-8.11	0.056337	123 -- 141	35 -- 53	D D-heptose 1 7-bisphosphate phosphatase	_____________122_________________142\n_____________\|___________________\|\n5'-AAA...AUCAG_____U____A________UCUUG...ACG-3'\n______________GUUUA_GCGA_GAGCACUU\n______________\|:\|\|\|_\|\|:\|_:\|\|\|\|\|\|\|\n______________CGAAU_CGUU_UUCGUGAA\n3'-UUU...UUGAA_____U____C________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	135 -- 141	35 -- 41	-19.8402 kcal/mol	5.62708 kcal/mol	6.10399 kcal/mol	122 142@LB@ \| \|@LB@5'-AAA...AUCAG U A UCUUG...ACG-3'@LB@ GUUUA GCGA GAGCACUU@LB@ \|:\|\|\| \|\|:\| :\|\|\|\|\|\|\|@LB@ CGAAU CGUU UUCGUGAA@LB@3'-UUU...UUGAA U C UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -19.8402 kcal/mol@LB@Unfolding Energy - mRNA 5.62708 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 123 -- 141@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 35 -- 41@LB@
163	0.0182	0.3566	b0397	sbcC	-8.10	0.056577	196 -- 210	26 -- 43	exonuclease dsDNA ATP-dependent	_____________195________________211\n_____________\|__________________\|\n5'-GAA...AACAC__________________UCAGC...UUG-3'\n______________GAAGCAU___GAAAAUUC\n______________\|\|\|\|\|\|:___:\|\|\|\|\|\|\|\n______________CUUCGUG___UUUUUAAG\n3'-UUU...UCGUU_______AAU________CAAUG...CAA-5'\n_____________\|__________________\|\n_____________44_________________25\n	204 -- 210	26 -- 32	-13.6528 kcal/mol	1.79109 kcal/mol	3.75931 kcal/mol	195 211@LB@ \| \|@LB@5'-GAA...AACAC UCAGC...UUG-3'@LB@ GAAGCAU GAAAAUUC@LB@ \|\|\|\|\|\|: :\|\|\|\|\|\|\|@LB@ CUUCGUG UUUUUAAG@LB@3'-UUU...UCGUU AAU CAAUG...CAA-5'@LB@ \| \|@LB@ 44 25@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -13.6528 kcal/mol@LB@Unfolding Energy - mRNA 1.79109 kcal/mol@LB@Unfolding Energy - sRNA 3.75931 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 26 -- 43@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 26 -- 32@LB@
116	0.009699	0.2693	b2708	srlQ	-8.08	0.057211	196 -- 214	36 -- 49	D-arabinose 5-phosphate isomerase	_____________195_________________215\n_____________\|___________________\|\n5'-UAC...GGAGA______UGAGU________ACUGA...GCG-3'\n______________GAGCAA_____GAAGCACU\n______________:\|\|\|\|\|_____\|\|\|\|\|\|\|\|\n______________UUCGUU_____CUUCGUGA\n3'-UUU...ACGAA___________________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________50__________________35\n	208 -- 214	36 -- 42	-17.2491 kcal/mol	3.12814 kcal/mol	6.03645 kcal/mol	195 215@LB@ \| \|@LB@5'-UAC...GGAGA UGAGU ACUGA...GCG-3'@LB@ GAGCAA GAAGCACU@LB@ :\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUCGUU CUUCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -17.2491 kcal/mol@LB@Unfolding Energy - mRNA 3.12814 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 196 -- 214@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 36 -- 42@LB@
20	0.0005034	0.08107	b3962	sthA	-8.00	0.060263	274 -- 291	37 -- 54	pyridine nucleotide transhydrogenase soluble	_____________273________________292\n_____________\|__________________\|\n5'-UAC...GGGCC__G__________U____GCGUC...CAG-3'\n______________UG_UUAAGCAAGG_GCGC\n______________\|\|_\|\|\|\|\|\|\|\|\|:_\|\|:\|\n______________AC_AAUUCGUUCU_CGUG\n3'-UUU...UUUGA__G__________U____AAUUU...CAA-5'\n_____________\|__________________\|\n_____________55_________________36\n	280 -- 286	42 -- 48	-21.3093 kcal/mol	7.14965 kcal/mol	6.1584 kcal/mol	273 292@LB@ \| \|@LB@5'-UAC...GGGCC G U GCGUC...CAG-3'@LB@ UG UUAAGCAAGG GCGC@LB@ \|\| \|\|\|\|\|\|\|\|\|: \|\|:\|@LB@ AC AAUUCGUUCU CGUG@LB@3'-UUU...UUUGA G U AAUUU...CAA-5'@LB@ \| \|@LB@ 55 36@LB@@LB@@LB@Energy -8.00 kcal/mol@LB@Hybridization Energy -21.3093 kcal/mol@LB@Unfolding Energy - mRNA 7.14965 kcal/mol@LB@Unfolding Energy - sRNA 6.1584 kcal/mol@LB@@LB@Position - mRNA 274 -- 291@LB@Position - sRNA 37 -- 54@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 42 -- 48@LB@
23	0.000685	0.09021	b3780	rhlB	-7.99	0.060609	254 -- 278	29 -- 60	ATP-dependent RNA helicase	_____________253______________________________279\n_____________\|________________________________\|\n5'-UCG...CAUCC____G_________________C_________AAAGG...CGC-3'\n______________GAAG_UUGU_______AGAAGC_CUUGAAAAA\n______________\|\|\|:_\|\|\|:_______\|\|\|\|\|\|_\|\|\|:\|\|\|\|\|\n______________CUUU_AACG_______UCUUCG_GAAUUUUUU\n3'-UUU...CCCUA____G____AAUUCGU______U_________AAGCA...CAA-5'\n_____________\|________________________________\|\n_____________61_______________________________28\n	270 -- 276	31 -- 37	-19.7636 kcal/mol	5.50064 kcal/mol	6.27092 kcal/mol	253 279@LB@ \| \|@LB@5'-UCG...CAUCC G C AAAGG...CGC-3'@LB@ GAAG UUGU AGAAGC CUUGAAAAA@LB@ \|\|\|: \|\|\|: \|\|\|\|\|\| \|\|\|:\|\|\|\|\|@LB@ CUUU AACG UCUUCG GAAUUUUUU@LB@3'-UUU...CCCUA G AAUUCGU U AAGCA...CAA-5'@LB@ \| \|@LB@ 61 28@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -19.7636 kcal/mol@LB@Unfolding Energy - mRNA 5.50064 kcal/mol@LB@Unfolding Energy - sRNA 6.27092 kcal/mol@LB@@LB@Position - mRNA 254 -- 278@LB@Position - sRNA 29 -- 60@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 31 -- 37@LB@
78	0.004685	0.1935	b3905	rhaS	-7.96	0.061746	70 -- 86	26 -- 40	transcriptional activator of rhaBAD and rhaT	_____________69________________87\n_____________\|_________________\|\n5'-UGG...UCACC______CCU________ACGCU...AUG-3'\n______________GCAUUU___GAAAAUUC\n______________\|\|\|:\|\|___:\|\|\|\|\|\|\|\n______________CGUGAA___UUUUUAAG\n3'-UUU...UUCUU______U__________CAAUG...CAA-5'\n_____________\|_________________\|\n_____________41________________25\n	80 -- 86	26 -- 32	-11.6625 kcal/mol	2.05222 kcal/mol	1.64811 kcal/mol	69 87@LB@ \| \|@LB@5'-UGG...UCACC CCU ACGCU...AUG-3'@LB@ GCAUUU GAAAAUUC@LB@ \|\|\|:\|\| :\|\|\|\|\|\|\|@LB@ CGUGAA UUUUUAAG@LB@3'-UUU...UUCUU U CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -11.6625 kcal/mol@LB@Unfolding Energy - mRNA 2.05222 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 70 -- 86@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 26 -- 32@LB@
38	0.00143	0.1212	b3315	rplV	-7.95	0.062235	2 -- 19	23 -- 40	50S ribosomal subunit protein L22	_____________1__________________20\n_____________\|__________________\|\n__________5'-C________UCCCG_____CAACG...UGG-3'\n______________GCACUUGG_____UCGUU\n______________\|\|\|\|\|\|::_____\|\|\|\|\|\n______________CGUGAAUU_____AGCAA\n3'-UUU...UUCUU________UUUUA_____UGUGG...CAA-5'\n_____________\|__________________\|\n_____________41_________________22\n	3 -- 9	33 -- 39	-14.4443 kcal/mol	4.84591 kcal/mol	1.64885 kcal/mol	1 20@LB@ \| \|@LB@ 5'-C UCCCG CAACG...UGG-3'@LB@ GCACUUGG UCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|@LB@ CGUGAAUU AGCAA@LB@3'-UUU...UUCUU UUUUA UGUGG...CAA-5'@LB@ \| \|@LB@ 41 22@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -14.4443 kcal/mol@LB@Unfolding Energy - mRNA 4.84591 kcal/mol@LB@Unfolding Energy - sRNA 1.64885 kcal/mol@LB@@LB@Position - mRNA 2 -- 19@LB@Position - sRNA 23 -- 40@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 33 -- 39@LB@
4	1.769e-05	0.01424	b2105	rcnR	-7.88	0.065143	12 -- 26	36 -- 49	transcriptional repressor of rcnA	_____________11______________27\n_____________\|_______________\|\n5'-UGA...GCACC________U______GGGGA...ACG-3'\n______________AAGUAAGA_GGCGCU\n______________\|\|\|:\|\|\|\|_:\|\|:\|\|\n______________UUCGUUCU_UCGUGA\n3'-UUU...ACGAA_______________AUUUU...CAA-5'\n_____________\|_______________\|\n_____________50______________35\n	13 -- 19	42 -- 48	-15.6635 kcal/mol	1.75127 kcal/mol	6.03645 kcal/mol	11 27@LB@ \| \|@LB@5'-UGA...GCACC U GGGGA...ACG-3'@LB@ AAGUAAGA GGCGCU@LB@ \|\|\|:\|\|\|\| :\|\|:\|\|@LB@ UUCGUUCU UCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -15.6635 kcal/mol@LB@Unfolding Energy - mRNA 1.75127 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 12 -- 26@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 42 -- 48@LB@
107	0.009263	0.2693	b3034	nudF	-7.86	0.065629	202 -- 214	42 -- 54	ADP-ribose pyrophosphatase	_____________201___________215\n_____________\|_____________\|\n5'-AUU...AACAA_________C___CAACC...UUU-3'\n______________UGCUUAAGC_AGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\n______________ACGAAUUCG_UCU\n3'-UUU...UUUGA_________U___UCGUG...CAA-5'\n_____________\|_____________\|\n_____________55____________41\n	204 -- 210	46 -- 52	-15.7149 kcal/mol	1.83586 kcal/mol	6.01534 kcal/mol	201 215@LB@ \| \|@LB@5'-AUU...AACAA C CAACC...UUU-3'@LB@ UGCUUAAGC AGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|@LB@ ACGAAUUCG UCU@LB@3'-UUU...UUUGA U UCGUG...CAA-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -15.7149 kcal/mol@LB@Unfolding Energy - mRNA 1.83586 kcal/mol@LB@Unfolding Energy - sRNA 6.01534 kcal/mol@LB@@LB@Position - mRNA 202 -- 214@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 46 -- 52@LB@
185	0.02171	0.3768	b0059	rapA	-7.86	0.065955	35 -- 74	2 -- 42	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase-associated ATP-dependent RNA translocase	_____________34___________________________________________75\n_____________\|____________________________________________\|\n5'-GCU...AUUUU_____AAAA__________CCAG______U___________C__GACGA...UUU-3'\n______________GAGCA____AAAGAGUUCG____AUACCA_____UUUGAUG_GU\n______________:\|\|\|\|____\|\|\|:\|:\|\|\|\|____\|:\|\|\|\|_____\|:\|\|\|\|\|_\|\|\n______________UUCGU____UUUUUUAAGC____UGUGGU_____AGACUAC_CA\n3'-UUU...CGUUC_____GAA___________AA________CCUUU_______A__A-5'\n_____________\|____________________________________________\|\n_____________43___________________________________________1\n	47 -- 53	25 -- 31	-26.2778 kcal/mol	9.20057 kcal/mol	9.22149 kcal/mol	34 75@LB@ \| \|@LB@5'-GCU...AUUUU AAAA CCAG U C GACGA...UUU-3'@LB@ GAGCA AAAGAGUUCG AUACCA UUUGAUG GU@LB@ :\|\|\|\| \|\|\|:\|:\|\|\|\| \|:\|\|\|\| \|:\|\|\|\|\| \|\|@LB@ UUCGU UUUUUUAAGC UGUGGU AGACUAC CA@LB@3'-UUU...CGUUC GAA AA CCUUU A A-5'@LB@ \| \|@LB@ 43 1@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -26.2778 kcal/mol@LB@Unfolding Energy - mRNA 9.20057 kcal/mol@LB@Unfolding Energy - sRNA 9.22149 kcal/mol@LB@@LB@Position - mRNA 35 -- 74@LB@Position - sRNA 2 -- 42@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 25 -- 31@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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