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
26	0.0002514	0.03403	b4551	yheV	-11.83	0.112444	191 -- 229	42 -- 77	DUF2387 family putative metal-binding protein	_____________190_____________________________________230\n_____________\|_______________________________________\|\n5'-AUC...GAGUA____G__A_G________C__AAAAC________GC___CGCAA...UUG-3'\n______________GAGG_UA_A_AUGGCAAU_CG_____GUUUUAUU__GGG\n______________:\|\|:_\|\|_\|_\|::\|\|\|\|\|_\|\|_____\|\|\|\|:\|:\|__\|\|\|\n______________UUCU_AU_U_UGUCGUUA_GC_____CAAAGUGA__CCC\n3'-UUU...CCCGU____G__G_G________A__AA___________GU___CUAAA...GCA-5'\n_____________\|_______________________________________\|\n_____________78______________________________________41\n	217 -- 223	48 -- 54	-24.6454 kcal/mol	8.05545 kcal/mol	4.7648 kcal/mol	190 230@LB@ \| \|@LB@5'-AUC...GAGUA G A G C AAAAC GC CGCAA...UUG-3'@LB@ GAGG UA A AUGGCAAU CG GUUUUAUU GGG@LB@ :\|\|: \|\| \| \|::\|\|\|\|\| \|\| \|\|\|\|:\|:\| \|\|\|@LB@ UUCU AU U UGUCGUUA GC CAAAGUGA CCC@LB@3'-UUU...CCCGU G G G A AA GU CUAAA...GCA-5'@LB@ \| \|@LB@ 78 41@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -24.6454 kcal/mol@LB@Unfolding Energy - mRNA 8.05545 kcal/mol@LB@Unfolding Energy - sRNA 4.7648 kcal/mol@LB@@LB@Position - mRNA 191 -- 229@LB@Position - sRNA 42 -- 77@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 48 -- 54@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@
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@
88	0.003962	0.1538	b3084	rlmG	-11.78	0.115170	185 -- 197	40 -- 51	23S rRNA m(2)G1835 methyltransferase SAM-dependent	_____________184___________198\n_____________\|_____________\|\n5'-UGU...UUUUA_________A___CCGAU...AAU-3'\n______________UCAUUCAGG_GGG\n______________\|\|\|:\|\|\|\|\|_\|\|:\n______________AGUGAGUCC_CCU\n3'-UUU...AACAA_____________AAAGG...GCA-5'\n_____________\|_____________\|\n_____________52____________39\n	187 -- 193	43 -- 49	-16.9089 kcal/mol	3.37488 kcal/mol	1.76028 kcal/mol	184 198@LB@ \| \|@LB@5'-UGU...UUUUA A CCGAU...AAU-3'@LB@ UCAUUCAGG GGG@LB@ \|\|\|:\|\|\|\|\| \|\|:@LB@ AGUGAGUCC CCU@LB@3'-UUU...AACAA AAAGG...GCA-5'@LB@ \| \|@LB@ 52 39@LB@@LB@@LB@Energy -11.78 kcal/mol@LB@Hybridization Energy -16.9089 kcal/mol@LB@Unfolding Energy - mRNA 3.37488 kcal/mol@LB@Unfolding Energy - sRNA 1.76028 kcal/mol@LB@@LB@Position - mRNA 185 -- 197@LB@Position - sRNA 40 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 43 -- 49@LB@
183	0.009087	0.1747	b3965	trmA	-11.75	0.116675	18 -- 52	35 -- 74	tRNA m(5)U54 methyltransferase SAM-dependent; tmRNA m(5)U341 methyltransferase	_____________17____________________________________________53\n_____________\|_____________________________________________\|\n5'-UCG...UUACC________U____UCCA_________________________C__UAUUA...UUC-3'\n______________GCUGCGCG_CAGC____GAUUCG______CACU____GGAUU_CC\n______________:\|\|:\|:\|:_\|\|\|\|____:\|\|\|\|\|______\|\|\|\|____\|\|\|\|\|_\|\|\n______________UGAUGUGU_GUCG____UUAAGC______GUGA____CCUAA_GG\n3'-UUU...GUUUC_______________________AACAAA____GUCC_____A__UACGA...GCA-5'\n_____________\|_____________________________________________\|\n_____________75____________________________________________34\n	18 -- 24	68 -- 74	-28.5766 kcal/mol	12.0258 kcal/mol	4.80541 kcal/mol	17 53@LB@ \| \|@LB@5'-UCG...UUACC U UCCA C UAUUA...UUC-3'@LB@ GCUGCGCG CAGC GAUUCG CACU GGAUU CC@LB@ :\|\|:\|:\|: \|\|\|\| :\|\|\|\|\| \|\|\|\| \|\|\|\|\| \|\|@LB@ UGAUGUGU GUCG UUAAGC GUGA CCUAA GG@LB@3'-UUU...GUUUC AACAAA GUCC A UACGA...GCA-5'@LB@ \| \|@LB@ 75 34@LB@@LB@@LB@Energy -11.75 kcal/mol@LB@Hybridization Energy -28.5766 kcal/mol@LB@Unfolding Energy - mRNA 12.0258 kcal/mol@LB@Unfolding Energy - sRNA 4.80541 kcal/mol@LB@@LB@Position - mRNA 18 -- 52@LB@Position - sRNA 35 -- 74@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 68 -- 74@LB@
60	0.002324	0.1363	b0881	clpS	-11.74	0.117068	9 -- 15	40 -- 46	regulatory protein for ClpA substrate specificity	_____________8_______16\n_____________\|_______\|\n___5'-GCAUUUGA_______CAAGG...UCA-3'\n______________CAGGGGA\n______________\|\|\|\|\|\|\|\n______________GUCCCCU\n3'-UUU...AGUGA_______AAAGG...GCA-5'\n_____________\|_______\|\n_____________47______39\n	9 -- 15	40 -- 46	-13.2936 kcal/mol	0.199257 kcal/mol	1.35582 kcal/mol	8 16@LB@ \| \|@LB@ 5'-GCAUUUGA CAAGG...UCA-3'@LB@ CAGGGGA@LB@ \|\|\|\|\|\|\|@LB@ GUCCCCU@LB@3'-UUU...AGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 47 39@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -13.2936 kcal/mol@LB@Unfolding Energy - mRNA 0.199257 kcal/mol@LB@Unfolding Energy - sRNA 1.35582 kcal/mol@LB@@LB@Position - mRNA 9 -- 15@LB@Position - sRNA 40 -- 46@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 40 -- 46@LB@
95	0.004386	0.1538	b1083	flgL	-11.72	0.118200	146 -- 194	40 -- 76	flagellar hook-filament junction protein	_____________145_________________________________________________195\n_____________\|___________________________________________________\|\n5'-UUG...UCUGC____G___A______________AUGCGCUGAUUAACA______A______GAUAA...GUA-3'\n______________AGAC_GCA_AC_GCGAUUU_UUG_______________UUCGCU_AGGGGA\n______________\|\|\|\|_:\|\|_\|\|_\|\|:\|\|\|:_\|\|\|_______________\|\|\|:\|\|_\|\|\|\|\|\|\n______________UCUG_UGU_UG_CGUUAAG_AAC_______________AAGUGA_UCCCCU\n3'-UUU...CCGUU____A___G__U_______C___A____________________G______AAAGG...GCA-5'\n_____________\|___________________________________________________\|\n_____________77__________________________________________________39\n	157 -- 163	58 -- 64	-28.9648 kcal/mol	12.4692 kcal/mol	4.77843 kcal/mol	145 195@LB@ \| \|@LB@5'-UUG...UCUGC G A AUGCGCUGAUUAACA A GAUAA...GUA-3'@LB@ AGAC GCA AC GCGAUUU UUG UUCGCU AGGGGA@LB@ \|\|\|\| :\|\| \|\| \|\|:\|\|\|: \|\|\| \|\|\|:\|\| \|\|\|\|\|\|@LB@ UCUG UGU UG CGUUAAG AAC AAGUGA UCCCCU@LB@3'-UUU...CCGUU A G U C A G AAAGG...GCA-5'@LB@ \| \|@LB@ 77 39@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -28.9648 kcal/mol@LB@Unfolding Energy - mRNA 12.4692 kcal/mol@LB@Unfolding Energy - sRNA 4.77843 kcal/mol@LB@@LB@Position - mRNA 146 -- 194@LB@Position - sRNA 40 -- 76@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 58 -- 64@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@
74	0.003066	0.1452	b0467	priC	-11.71	0.118543	157 -- 193	43 -- 75	primosomal replication protein N''	_____________156___________________________________194\n_____________\|_____________________________________\|\n5'-GGG...AGAGU______UUUA_____A_____AUCAU_______G___UCUUA...GUU-3'\n______________GGCUAC____GCAUA_CAAUU_____UUUCAUU_AGG\n______________\|:\|\|\|\|____:\|\|:\|_\|\|\|\|\|_____\|\|\|\|\|:\|_\|\|\|\n______________CUGAUG____UGUGU_GUUAA_____AAAGUGA_UCC\n3'-UUU...CGUUU_______________C_____GCAAC_______G___CCUAA...GCA-5'\n_____________\|_____________________________________\|\n_____________76____________________________________42\n	183 -- 189	47 -- 53	-24.815 kcal/mol	8.75149 kcal/mol	4.35266 kcal/mol	156 194@LB@ \| \|@LB@5'-GGG...AGAGU UUUA A AUCAU G UCUUA...GUU-3'@LB@ GGCUAC GCAUA CAAUU UUUCAUU AGG@LB@ \|:\|\|\|\| :\|\|:\| \|\|\|\|\| \|\|\|\|\|:\| \|\|\|@LB@ CUGAUG UGUGU GUUAA AAAGUGA UCC@LB@3'-UUU...CGUUU C GCAAC G CCUAA...GCA-5'@LB@ \| \|@LB@ 76 42@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -24.815 kcal/mol@LB@Unfolding Energy - mRNA 8.75149 kcal/mol@LB@Unfolding Energy - sRNA 4.35266 kcal/mol@LB@@LB@Position - mRNA 157 -- 193@LB@Position - sRNA 43 -- 75@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 47 -- 53@LB@
67	0.002719	0.1417	b3454	livF	-11.67	0.120634	106 -- 122	40 -- 58	branched-chain amino acid ABC transporter ATPase	_____________105_________________123\n_____________\|___________________\|\n5'-AGA...AUUUA___GG_____A________CGCCG...UUG-3'\n______________CGU____UCA_UCAGGGGA\n______________\|\|\|____\|\|\|_\|\|\|\|\|\|\|\|\n______________GCA____AGU_AGUCCCCU\n3'-UUU...GUUAA___ACAA___G________AAAGG...GCA-5'\n_____________\|___________________\|\n_____________59__________________39\n	116 -- 122	40 -- 46	-19.8465 kcal/mol	5.75116 kcal/mol	2.42241 kcal/mol	105 123@LB@ \| \|@LB@5'-AGA...AUUUA GG A CGCCG...UUG-3'@LB@ CGU UCA UCAGGGGA@LB@ \|\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GCA AGU AGUCCCCU@LB@3'-UUU...GUUAA ACAA G AAAGG...GCA-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -19.8465 kcal/mol@LB@Unfolding Energy - mRNA 5.75116 kcal/mol@LB@Unfolding Energy - sRNA 2.42241 kcal/mol@LB@@LB@Position - mRNA 106 -- 122@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 40 -- 46@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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