Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
131	0.005914	0.1577	b2360	yfdQ	-15.68	0.013816	114 -- 143	46 -- 74	CPS-53 (KpLE1) prophage; uncharacterized protein	_____________113____________________________144\n_____________\|______________________________\|\n5'-UCC...GGAAA___C__________G__AUUAAUA______UUAAU...CUG-3'\n______________ACU_CGCGCAGCAG_UC_______UCAUUC\n______________\|\|\|_\|:\|:\|\|\|\|\|:_\|\|_______\|\|\|:\|\|\n______________UGA_GUGUGUCGUU_AG_______AGUGAG\n3'-UUU...GUUUC___U__________A__CAACAA_______UCCCC...GCA-5'\n_____________\|______________________________\|\n_____________75_____________________________45\n	121 -- 127	61 -- 67	-23.4619 kcal/mol	4.06011 kcal/mol	3.72594 kcal/mol	113 144@LB@ \| \|@LB@5'-UCC...GGAAA C G AUUAAUA UUAAU...CUG-3'@LB@ ACU CGCGCAGCAG UC UCAUUC@LB@ \|\|\| \|:\|:\|\|\|\|\|: \|\| \|\|\|:\|\|@LB@ UGA GUGUGUCGUU AG AGUGAG@LB@3'-UUU...GUUUC U A CAACAA UCCCC...GCA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -23.4619 kcal/mol@LB@Unfolding Energy - mRNA 4.06011 kcal/mol@LB@Unfolding Energy - sRNA 3.72594 kcal/mol@LB@@LB@Position - mRNA 114 -- 143@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 61 -- 67@LB@
132	0.005915	0.1577	b3356	yhfA	-11.83	0.112173	273 -- 293	39 -- 71	OsmC family protein	_____________272_______________________________294\n_____________\|_________________________________\|\n5'-CUG...UUUUA___G_________________________C___AAAGCAC-3'\n______________AUG_ACGGCA____________ACUCAGG_GAU\n______________\|::_\|\|:\|\|\|____________\|\|\|\|\|\|\|_\|\|\|\n______________UGU_UGUCGU____________UGAGUCC_CUA\n3'-UUU...UCUGA___G______UAAGCAACAAAG_______C___AAGGU...GCA-5'\n_____________\|_________________________________\|\n_____________72________________________________38\n	283 -- 289	43 -- 49	-20.9729 kcal/mol	4.393 kcal/mol	4.74947 kcal/mol	272 294@LB@ \| \|@LB@5'-CUG...UUUUA G C AAAGCAC-3'@LB@ AUG ACGGCA ACUCAGG GAU@LB@ \|:: \|\|:\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UGU UGUCGU UGAGUCC CUA@LB@3'-UUU...UCUGA G UAAGCAACAAAG C AAGGU...GCA-5'@LB@ \| \|@LB@ 72 38@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -20.9729 kcal/mol@LB@Unfolding Energy - mRNA 4.393 kcal/mol@LB@Unfolding Energy - sRNA 4.74947 kcal/mol@LB@@LB@Position - mRNA 273 -- 293@LB@Position - sRNA 39 -- 71@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 43 -- 49@LB@
133	0.006126	0.1605	b0387	yaiI	-9.01	0.350598	46 -- 81	33 -- 74	UPF0178 family protein	_____________45_________________________________________82\n_____________\|__________________________________________\|\n5'-CAC...CCCAU____________CAAUAAAACCG______UCU__________UGCCU...CAA-3'\n______________AUUGC_CGCAGC_____________AUUU______UUUCCAU\n______________\|:\|:\|_\|:\|\|\|\|_____________\|:\|:______\|\|\|\|\|\|\|\n______________UGAUG_GUGUCG_____________UGAG______AAAGGUA\n3'-UUU...GUUUC_____U______UUAAGCAACAAAG____UCCCCU_______CGAAU...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________32\n	75 -- 81	33 -- 39	-16.9561 kcal/mol	3.12923 kcal/mol	4.81602 kcal/mol	45 82@LB@ \| \|@LB@5'-CAC...CCCAU CAAUAAAACCG UCU UGCCU...CAA-3'@LB@ AUUGC CGCAGC AUUU UUUCCAU@LB@ \|:\|:\| \|:\|\|\|\| \|:\|: \|\|\|\|\|\|\|@LB@ UGAUG GUGUCG UGAG AAAGGUA@LB@3'-UUU...GUUUC U UUAAGCAACAAAG UCCCCU CGAAU...GCA-5'@LB@ \| \|@LB@ 75 32@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -16.9561 kcal/mol@LB@Unfolding Energy - mRNA 3.12923 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 46 -- 81@LB@Position - sRNA 33 -- 74@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 33 -- 39@LB@
134	0.006141	0.1605	b3413	gntX	-10.72	0.183370	226 -- 267	37 -- 75	DNA catabolic protein	_____________225__________________________________________268\n_____________\|____________________________________________\|\n5'-CCC...AUGCU___________AAU__CACUGG____AGG_______________GUUCG...AUA-3'\n______________GGCUAUGC_CG___GC______CGUU___UCAUU_GGGGGAUUU\n______________\|:\|\|\|::\|_\|:___\|\|______\|\|\|\|___\|\|\|:\|_:\|\|\|\|\|\|\|\|\n______________CUGAUGUG_GU___CG______GCAA___AGUGA_UCCCCUAAA\n3'-UUU...CGUUU________U_______UUAA______CAA_____G_________GGUAC...GCA-5'\n_____________\|____________________________________________\|\n_____________76___________________________________________36\n	261 -- 267	37 -- 43	-30.3916 kcal/mol	14.8943 kcal/mol	4.77966 kcal/mol	225 268@LB@ \| \|@LB@5'-CCC...AUGCU AAU CACUGG AGG GUUCG...AUA-3'@LB@ GGCUAUGC CG GC CGUU UCAUU GGGGGAUUU@LB@ \|:\|\|\|::\| \|: \|\| \|\|\|\| \|\|\|:\| :\|\|\|\|\|\|\|\|@LB@ CUGAUGUG GU CG GCAA AGUGA UCCCCUAAA@LB@3'-UUU...CGUUU U UUAA CAA G GGUAC...GCA-5'@LB@ \| \|@LB@ 76 36@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -30.3916 kcal/mol@LB@Unfolding Energy - mRNA 14.8943 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 226 -- 267@LB@Position - sRNA 37 -- 75@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 37 -- 43@LB@
135	0.006184	0.1605	b0637	rsfS	-13.92	0.038847	179 -- 195	40 -- 56	ribosomal silencing factor	_____________178_______________196\n_____________\|_________________\|\n5'-AUU...UCUAU___A_____C_______AAAAC...UCA-3'\n______________UUG_UUCAC_CAGGGGG\n______________\|\|\|_\|\|\|\|\|_\|\|\|\|\|\|:\n______________AAC_AAGUG_GUCCCCU\n3'-UUU...UAAGC___A_____A_______AAAGG...GCA-5'\n_____________\|_________________\|\n_____________57________________39\n	189 -- 195	40 -- 46	-20.5369 kcal/mol	4.69018 kcal/mol	1.92548 kcal/mol	178 196@LB@ \| \|@LB@5'-AUU...UCUAU A C AAAAC...UCA-3'@LB@ UUG UUCAC CAGGGGG@LB@ \|\|\| \|\|\|\|\| \|\|\|\|\|\|:@LB@ AAC AAGUG GUCCCCU@LB@3'-UUU...UAAGC A A AAAGG...GCA-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -20.5369 kcal/mol@LB@Unfolding Energy - mRNA 4.69018 kcal/mol@LB@Unfolding Energy - sRNA 1.92548 kcal/mol@LB@@LB@Position - mRNA 179 -- 195@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 40 -- 46@LB@
136	0.006258	0.1605	b0219	yafV	-11.82	0.112632	212 -- 233	61 -- 78	putative NAD(P)-binding C-N hydrolase family amidase	_____________211____________________234\n_____________\|______________________\|\n5'-GUC...GGUUU___________UUUU_______CCACU...CCG-3'\n______________GAAGAUUACGC____GCAGCAA\n______________:\|\|\|\|:\|\|\|:\|____:\|\|\|\|\|\|\n______________UUUCUGAUGUG____UGUCGUU\n3'-UUU...ACCCG______________________AAGCA...GCA-5'\n_____________\|______________________\|\n_____________79_____________________60\n	227 -- 233	61 -- 67	-20.0989 kcal/mol	5.01896 kcal/mol	3.25783 kcal/mol	211 234@LB@ \| \|@LB@5'-GUC...GGUUU UUUU CCACU...CCG-3'@LB@ GAAGAUUACGC GCAGCAA@LB@ :\|\|\|\|:\|\|\|:\| :\|\|\|\|\|\|@LB@ UUUCUGAUGUG UGUCGUU@LB@3'-UUU...ACCCG AAGCA...GCA-5'@LB@ \| \|@LB@ 79 60@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -20.0989 kcal/mol@LB@Unfolding Energy - mRNA 5.01896 kcal/mol@LB@Unfolding Energy - sRNA 3.25783 kcal/mol@LB@@LB@Position - mRNA 212 -- 233@LB@Position - sRNA 61 -- 78@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 61 -- 67@LB@
137	0.006282	0.1605	b0123	cueO	-13.57	0.047118	144 -- 176	48 -- 78	multicopper oxidase (laccase)	_____________143________________________________177\n_____________\|__________________________________\|\n5'-CUG...AGGGG___________U__A_______AUU_________CUGCU...CGU-3'\n______________AAGGACUAUGC_CA_C_GUUUG___UUGUUUCGC\n______________\|\|:\|\|\|\|\|::\|_\|\|_\|_:\|\|:\|___\|\|\|\|\|\|\|:\|\n______________UUUCUGAUGUG_GU_G_UAAGC___AACAAAGUG\n3'-UUU...ACCCG___________U__C_U_________________AGUCC...GCA-5'\n_____________\|__________________________________\|\n_____________79_________________________________47\n	170 -- 176	48 -- 54	-24.1368 kcal/mol	6.88378 kcal/mol	3.68736 kcal/mol	143 177@LB@ \| \|@LB@5'-CUG...AGGGG U A AUU CUGCU...CGU-3'@LB@ AAGGACUAUGC CA C GUUUG UUGUUUCGC@LB@ \|\|:\|\|\|\|\|::\| \|\| \| :\|\|:\| \|\|\|\|\|\|\|:\|@LB@ UUUCUGAUGUG GU G UAAGC AACAAAGUG@LB@3'-UUU...ACCCG U C U AGUCC...GCA-5'@LB@ \| \|@LB@ 79 47@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -24.1368 kcal/mol@LB@Unfolding Energy - mRNA 6.88378 kcal/mol@LB@Unfolding Energy - sRNA 3.68736 kcal/mol@LB@@LB@Position - mRNA 144 -- 176@LB@Position - sRNA 48 -- 78@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 48 -- 54@LB@
138	0.006392	0.1605	b0345	lacI	-7.62	0.533808	7 -- 17	61 -- 71	lactose-inducible lac operon transcriptional repressor	_____________6___________18\n_____________\|___________\|\n_____5'-CAUUGA___G_______AAAAG...AAA-3'\n______________ACA_GCAGCGG\n______________\|\|\|_:\|\|\|\|::\n______________UGU_UGUCGUU\n3'-UUU...UCUGA___G_______AAGCA...GCA-5'\n_____________\|___________\|\n_____________72__________60\n	11 -- 17	61 -- 67	-13.1569 kcal/mol	2.35774 kcal/mol	3.17655 kcal/mol	6 18@LB@ \| \|@LB@ 5'-CAUUGA G AAAAG...AAA-3'@LB@ ACA GCAGCGG@LB@ \|\|\| :\|\|\|\|::@LB@ UGU UGUCGUU@LB@3'-UUU...UCUGA G AAGCA...GCA-5'@LB@ \| \|@LB@ 72 60@LB@@LB@@LB@Energy -7.62 kcal/mol@LB@Hybridization Energy -13.1569 kcal/mol@LB@Unfolding Energy - mRNA 2.35774 kcal/mol@LB@Unfolding Energy - sRNA 3.17655 kcal/mol@LB@@LB@Position - mRNA 7 -- 17@LB@Position - sRNA 61 -- 71@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 61 -- 67@LB@
139	0.006425	0.1605	b0924	mukB	-11.72	0.118276	203 -- 227	45 -- 75	chromosome condensin MukBEF ATPase and DNA-binding subunit	_____________202_____________________________228\n_____________\|_______________________________\|\n5'-UGG...AUAAU_____A_________A_______________CUGAC...CUG-3'\n______________GAUUG_ACGCGGUAA_______UUUCGCUCA\n______________\|\|:\|:_\|\|:\|:\|:\|\|_______\|\|\|\|:\|\|\|\|\n______________CUGAU_UGUGUCGUU_______AAAGUGAGU\n3'-UUU...CGUUU_____G_________AAGCAAC_________CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	221 -- 227	45 -- 51	-22.3255 kcal/mol	6.8688 kcal/mol	3.74078 kcal/mol	202 228@LB@ \| \|@LB@5'-UGG...AUAAU A A CUGAC...CUG-3'@LB@ GAUUG ACGCGGUAA UUUCGCUCA@LB@ \|\|:\|: \|\|:\|:\|:\|\| \|\|\|\|:\|\|\|\|@LB@ CUGAU UGUGUCGUU AAAGUGAGU@LB@3'-UUU...CGUUU G AAGCAAC CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -22.3255 kcal/mol@LB@Unfolding Energy - mRNA 6.8688 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 203 -- 227@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 45 -- 51@LB@
140	0.006445	0.1605	b0325	yahK	-13.93	0.038719	67 -- 79	43 -- 55	broad specificity NADPH-dependent aldehyde reductase Zn-containing	_____________66____________80\n_____________\|_____________\|\n5'-UUA...UGCUC_____________CUCGC...AAA-3'\n______________UGUUUCAUUCAGG\n______________\|\|\|\|\|\|\|:\|\|\|\|\|\n______________ACAAAGUGAGUCC\n3'-UUU...AAGCA_____________CCUAA...GCA-5'\n_____________\|_____________\|\n_____________56____________42\n	73 -- 79	43 -- 49	-18.9036 kcal/mol	3.47822 kcal/mol	1.49792 kcal/mol	66 80@LB@ \| \|@LB@5'-UUA...UGCUC CUCGC...AAA-3'@LB@ UGUUUCAUUCAGG@LB@ \|\|\|\|\|\|\|:\|\|\|\|\|@LB@ ACAAAGUGAGUCC@LB@3'-UUU...AAGCA CCUAA...GCA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -13.93 kcal/mol@LB@Hybridization Energy -18.9036 kcal/mol@LB@Unfolding Energy - mRNA 3.47822 kcal/mol@LB@Unfolding Energy - sRNA 1.49792 kcal/mol@LB@@LB@Position - mRNA 67 -- 79@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 43 -- 49@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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