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
173	0.008582	0.1745	b0060	polB	-11.19	0.150164	8 -- 23	39 -- 51	DNA polymerase II	_____________7________________24\n_____________\|________________\|\n____5'-GAAGAGG_______UAU______AUUCU...AGG-3'\n______________UCGCUUA___GGGGAU\n______________\|\|:\|\|:\|___\|\|\|\|\|\|\n______________AGUGAGU___CCCCUA\n3'-UUU...AACAA________________AAGGU...GCA-5'\n_____________\|________________\|\n_____________52_______________38\n	8 -- 14	45 -- 51	-16.4647 kcal/mol	3.48224 kcal/mol	1.79807 kcal/mol	7 24@LB@ \| \|@LB@ 5'-GAAGAGG UAU AUUCU...AGG-3'@LB@ UCGCUUA GGGGAU@LB@ \|\|:\|\|:\| \|\|\|\|\|\|@LB@ AGUGAGU CCCCUA@LB@3'-UUU...AACAA AAGGU...GCA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -16.4647 kcal/mol@LB@Unfolding Energy - mRNA 3.48224 kcal/mol@LB@Unfolding Energy - sRNA 1.79807 kcal/mol@LB@@LB@Position - mRNA 8 -- 23@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 45 -- 51@LB@
24	0.0002076	0.02926	b3459	panM	-18.00	0.002751	9 -- 48	38 -- 75	PanD autocleavage accelerator panothenate synthesis	_____________8___________________________________________49\n_____________\|___________________________________________\|\n___5'-AAAAUAAC_______A_G___GGAAU_____ACUA________________AUGCU...UUG-3'\n______________GGC_ACA_A_GGC_____AAUUC______UCAUUCAGGGGAUU\n______________\|:\|_\|\|\|_\|_:\|\|_____\|\|\|\|\|______\|\|\|:\|\|\|\|\|\|\|\|\|\|\n______________CUG_UGU_U_UCG_____UUAAG______AGUGAGUCCCCUAA\n3'-UUU...CGUUU___A___G_G_____________CAACAA______________AGGUA...GCA-5'\n_____________\|___________________________________________\|\n_____________76__________________________________________37\n	42 -- 48	38 -- 44	-31.5918 kcal/mol	8.81239 kcal/mol	4.77946 kcal/mol	8 49@LB@ \| \|@LB@ 5'-AAAAUAAC A G GGAAU ACUA AUGCU...UUG-3'@LB@ GGC ACA A GGC AAUUC UCAUUCAGGGGAUU@LB@ \|:\| \|\|\| \| :\|\| \|\|\|\|\| \|\|\|:\|\|\|\|\|\|\|\|\|\|@LB@ CUG UGU U UCG UUAAG AGUGAGUCCCCUAA@LB@3'-UUU...CGUUU A G G CAACAA AGGUA...GCA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -31.5918 kcal/mol@LB@Unfolding Energy - mRNA 8.81239 kcal/mol@LB@Unfolding Energy - sRNA 4.77946 kcal/mol@LB@@LB@Position - mRNA 9 -- 48@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 38 -- 44@LB@
47	0.001402	0.105	b2297	pta	-18.38	0.002042	9 -- 40	45 -- 75	phosphate acetyltransferase	_____________8__________________________________41\n_____________\|__________________________________\|\n___5'-CGCAACCU_________UUU______A__UG___________ACAAA...GUC-3'\n______________GGCUGCACG___CGGCAA_UC___GUUUCA_UCA\n______________\|:\|\|:\|\|\|:___\|:\|\|\|\|_\|\|___\|\|\|\|\|\|_\|\|\|\n______________CUGAUGUGU___GUCGUU_AG___CAAAGU_AGU\n3'-UUU...CGUUU__________________A__CAA______G___CCCCU...GCA-5'\n_____________\|__________________________________\|\n_____________76_________________________________44\n	11 -- 17	67 -- 73	-26.9548 kcal/mol	4.83173 kcal/mol	3.74078 kcal/mol	8 41@LB@ \| \|@LB@ 5'-CGCAACCU UUU A UG ACAAA...GUC-3'@LB@ GGCUGCACG CGGCAA UC GUUUCA UCA@LB@ \|:\|\|:\|\|\|: \|:\|\|\|\| \|\| \|\|\|\|\|\| \|\|\|@LB@ CUGAUGUGU GUCGUU AG CAAAGU AGU@LB@3'-UUU...CGUUU A CAA G CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -18.38 kcal/mol@LB@Hybridization Energy -26.9548 kcal/mol@LB@Unfolding Energy - mRNA 4.83173 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 9 -- 40@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 67 -- 73@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@
187	0.009506	0.1776	b1243	oppA	-10.52	0.199375	11 -- 17	40 -- 46	oligopeptide ABC transporter periplasmic binding protein	_____________10______18\n_____________\|_______\|\n5'-UGU...CUCGA_______GACAC...UCA-3'\n______________CAGGGGA\n______________\|\|\|\|\|\|\|\n______________GUCCCCU\n3'-UUU...AGUGA_______AAAGG...GCA-5'\n_____________\|_______\|\n_____________47______39\n	11 -- 17	40 -- 46	-13.6251 kcal/mol	1.75344 kcal/mol	1.35582 kcal/mol	10 18@LB@ \| \|@LB@5'-UGU...CUCGA GACAC...UCA-3'@LB@ CAGGGGA@LB@ \|\|\|\|\|\|\|@LB@ GUCCCCU@LB@3'-UUU...AGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 47 39@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -13.6251 kcal/mol@LB@Unfolding Energy - mRNA 1.75344 kcal/mol@LB@Unfolding Energy - sRNA 1.35582 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 40 -- 46@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 40 -- 46@LB@
102	0.004593	0.1538	b0343	lacY	-16.22	0.009713	12 -- 55	39 -- 78	lactose permease	_____________11___________________________________________56\n_____________\|____________________________________________\|\n5'-UGC...ACGCG_____AG_________UG___A___ACG_____CA_AU______UGGUG...GGC-3'\n______________GAAGA__GCACAUGGC__AAU_UCG___GUUUC__U__GGGGAU\n______________:\|\|\|\|__:\|\|\|\|::\|\|__\|\|\|_\|\|\|___\|\|\|\|\|__\|__\|\|\|\|\|\|\n______________UUUCU__UGUGUGUCG__UUA_AGC___CAAAG__A__CCCCUA\n3'-UUU...ACCCG_____GA__________________AA______UG_GU______AAGGU...GCA-5'\n_____________\|____________________________________________\|\n_____________79___________________________________________38\n	21 -- 27	63 -- 69	-31.4377 kcal/mol	10.4352 kcal/mol	4.77966 kcal/mol	11 56@LB@ \| \|@LB@5'-UGC...ACGCG AG UG A ACG CA AU UGGUG...GGC-3'@LB@ GAAGA GCACAUGGC AAU UCG GUUUC U GGGGAU@LB@ :\|\|\|\| :\|\|\|\|::\|\| \|\|\| \|\|\| \|\|\|\|\| \| \|\|\|\|\|\|@LB@ UUUCU UGUGUGUCG UUA AGC CAAAG A CCCCUA@LB@3'-UUU...ACCCG GA AA UG GU AAGGU...GCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -31.4377 kcal/mol@LB@Unfolding Energy - mRNA 10.4352 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 12 -- 55@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 63 -- 69@LB@
189	0.009605	0.1776	b0927	ycbL	-15.21	0.018444	14 -- 51	33 -- 78	putative metal-binding enzyme	_____________13__________________________________________________52\n_____________\|___________________________________________________\|\n5'-GGA...GAAGA________U_____UAAAG__________________CGAU__________AUUGA...GCG-3'\n______________AAAG_CUA_CACAC________________GC_CAGG____GGAUUUCCAU\n______________\|\|\|\|_\|\|\|_\|\|\|\|\|________________:\|_\|\|\|\|____\|\|\|\|\|\|\|\|\|\|\n______________UUUC_GAU_GUGUG________________UG_GUCC____CCUAAAGGUA\n3'-UUU...ACCCG____U_________UCGUUAAGCAACAAAG__A__________________CGAAU...GCA-5'\n_____________\|___________________________________________________\|\n_____________79__________________________________________________32\n	45 -- 51	33 -- 39	-26.8189 kcal/mol	6.79395 kcal/mol	4.81602 kcal/mol	13 52@LB@ \| \|@LB@5'-GGA...GAAGA U UAAAG CGAU AUUGA...GCG-3'@LB@ AAAG CUA CACAC GC CAGG GGAUUUCCAU@LB@ \|\|\|\| \|\|\| \|\|\|\|\| :\| \|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UUUC GAU GUGUG UG GUCC CCUAAAGGUA@LB@3'-UUU...ACCCG U UCGUUAAGCAACAAAG A CGAAU...GCA-5'@LB@ \| \|@LB@ 79 32@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -26.8189 kcal/mol@LB@Unfolding Energy - mRNA 6.79395 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 14 -- 51@LB@Position - sRNA 33 -- 78@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 33 -- 39@LB@
148	0.006951	0.1638	b3995	rsd	-9.56	0.289012	16 -- 28	58 -- 70	stationary phase protein binds sigma 70 RNA polymerase subunit	_____________15____________29\n_____________\|_____________\|\n5'-AAU...UUCGC_____________UCCCU...ACU-3'\n______________CAUAUGGCAAUUC\n______________\|\|:\|::\|\|\|\|\|\|\|\n______________GUGUGUCGUUAAG\n3'-UUU...CUGAU_____________CAACA...GCA-5'\n_____________\|_____________\|\n_____________71____________57\n	22 -- 28	58 -- 64	-15.8606 kcal/mol	3.09015 kcal/mol	3.21169 kcal/mol	15 29@LB@ \| \|@LB@5'-AAU...UUCGC UCCCU...ACU-3'@LB@ CAUAUGGCAAUUC@LB@ \|\|:\|::\|\|\|\|\|\|\|@LB@ GUGUGUCGUUAAG@LB@3'-UUU...CUGAU CAACA...GCA-5'@LB@ \| \|@LB@ 71 57@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -15.8606 kcal/mol@LB@Unfolding Energy - mRNA 3.09015 kcal/mol@LB@Unfolding Energy - sRNA 3.21169 kcal/mol@LB@@LB@Position - mRNA 16 -- 28@LB@Position - sRNA 58 -- 70@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 58 -- 64@LB@
200	0.01028	0.1776	b2803	fucK	-15.72	0.013449	16 -- 30	62 -- 76	L-fuculokinase	_____________15______________31\n_____________\|_______________\|\n5'-AUC...UGCCU_______________UGGAU...CGC-3'\n______________GGGCUGCGCACGGCA\n______________:\|:\|\|:\|:\|\|\|:\|\|\|\n______________UCUGAUGUGUGUCGU\n3'-UUU...CCGUU_______________UAAGC...GCA-5'\n_____________\|_______________\|\n_____________77______________61\n	24 -- 30	62 -- 68	-24.6836 kcal/mol	5.71098 kcal/mol	3.25371 kcal/mol	15 31@LB@ \| \|@LB@5'-AUC...UGCCU UGGAU...CGC-3'@LB@ GGGCUGCGCACGGCA@LB@ :\|:\|\|:\|:\|\|\|:\|\|\|@LB@ UCUGAUGUGUGUCGU@LB@3'-UUU...CCGUU UAAGC...GCA-5'@LB@ \| \|@LB@ 77 61@LB@@LB@@LB@Energy -15.72 kcal/mol@LB@Hybridization Energy -24.6836 kcal/mol@LB@Unfolding Energy - mRNA 5.71098 kcal/mol@LB@Unfolding Energy - sRNA 3.25371 kcal/mol@LB@@LB@Position - mRNA 16 -- 30@LB@Position - sRNA 62 -- 76@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 62 -- 68@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@

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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