Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
36	0.006672	0.5385	b3956	ppc	-10.31	0.093393	270 -- 282	76 -- 88	phosphoenolpyruvate carboxylase	_____________269___________283\n_____________\|_____________\|\n5'-CUU...CCAUC___GA________GAGAA...AAC-3'\n______________AAG__UGCGUUGG\n______________\|\|\|__::\|\|\|\|\|\|\n______________UUC__GUGCAACC\n3'-CGC...GCGUU___AA________GAAAU...AAG-5'\n_____________\|_____________\|\n_____________89____________75\n	276 -- 282	76 -- 82	-12.0501 kcal/mol	1.22517 kcal/mol	0.512479 kcal/mol	269 283@LB@ \| \|@LB@5'-CUU...CCAUC GA GAGAA...AAC-3'@LB@ AAG UGCGUUGG@LB@ \|\|\| ::\|\|\|\|\|\|@LB@ UUC GUGCAACC@LB@3'-CGC...GCGUU AA GAAAU...AAG-5'@LB@ \| \|@LB@ 89 75@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -12.0501 kcal/mol@LB@Unfolding Energy - mRNA 1.22517 kcal/mol@LB@Unfolding Energy - sRNA 0.512479 kcal/mol@LB@@LB@Position - mRNA 270 -- 282@LB@Position - sRNA 76 -- 88@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 76 -- 82@LB@
124	0.02124	0.5385	b0198	metI	-9.85	0.112177	270 -- 285	71 -- 87	DL-methionine transporter subunit	_____________269_______________286\n_____________\|_________________\|\n5'-UCA...UAUCC_____UU__________UGAUU...CGG-3'\n______________GGUUU___UUGGCUUUG\n______________:\|\|\|:___\|\|\|\|\|\|\|\|:\n______________UCAAG___AACCGAAAU\n3'-CGC...CGUUU_____UGC_________CAAUA...AAG-5'\n_____________\|_________________\|\n_____________88________________70\n	279 -- 285	71 -- 77	-13.0228 kcal/mol	2.60961 kcal/mol	0.562376 kcal/mol	269 286@LB@ \| \|@LB@5'-UCA...UAUCC UU UGAUU...CGG-3'@LB@ GGUUU UUGGCUUUG@LB@ :\|\|\|: \|\|\|\|\|\|\|\|:@LB@ UCAAG AACCGAAAU@LB@3'-CGC...CGUUU UGC CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -13.0228 kcal/mol@LB@Unfolding Energy - mRNA 2.60961 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 270 -- 285@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 71 -- 77@LB@
75	0.01364	0.5385	b0107	hofB	-15.68	0.010425	272 -- 289	69 -- 87	T2SE secretion family protein; P-loop ATPase superfamily protein	_____________271_________________290\n_____________\|___________________\|\n5'-CCA...GAGGU_____________GG____CGAUG...CUU-3'\n______________GGUUCAUGUUG_C__UAGU\n______________:\|\|\|\|\|:\|\|\|\|_\|__\|\|\|\|\n______________UCAAGUGCAAC_G__AUCA\n3'-CGC...CGUUU___________C_AA____AUAAG...AAG-5'\n_____________\|___________________\|\n_____________88__________________68\n	276 -- 282	77 -- 83	-18.3354 kcal/mol	2.08484 kcal/mol	0.569189 kcal/mol	271 290@LB@ \| \|@LB@5'-CCA...GAGGU GG CGAUG...CUU-3'@LB@ GGUUCAUGUUG C UAGU@LB@ :\|\|\|\|\|:\|\|\|\| \| \|\|\|\|@LB@ UCAAGUGCAAC G AUCA@LB@3'-CGC...CGUUU C AA AUAAG...AAG-5'@LB@ \| \|@LB@ 88 68@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -18.3354 kcal/mol@LB@Unfolding Energy - mRNA 2.08484 kcal/mol@LB@Unfolding Energy - sRNA 0.569189 kcal/mol@LB@@LB@Position - mRNA 272 -- 289@LB@Position - sRNA 69 -- 87@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 77 -- 83@LB@
158	0.02721	0.5559	b1724	ydiZ	-8.58	0.183444	272 -- 279	57 -- 64	uncharacterized protein	_____________271______280\n_____________\|________\|\n5'-UUU...AUUAA________AUAAU...ACG-3'\n______________CGAGUUGA\n______________\|\|\|\|\|\|\|\|\n______________GCUCAACU\n3'-CGC...AAUAA________CUUUG...AAG-5'\n_____________\|________\|\n_____________65_______56\n	273 -- 279	57 -- 63	-11.4752 kcal/mol	1.7639 kcal/mol	1.12823 kcal/mol	271 280@LB@ \| \|@LB@5'-UUU...AUUAA AUAAU...ACG-3'@LB@ CGAGUUGA@LB@ \|\|\|\|\|\|\|\|@LB@ GCUCAACU@LB@3'-CGC...AAUAA CUUUG...AAG-5'@LB@ \| \|@LB@ 65 56@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -11.4752 kcal/mol@LB@Unfolding Energy - mRNA 1.7639 kcal/mol@LB@Unfolding Energy - sRNA 1.12823 kcal/mol@LB@@LB@Position - mRNA 272 -- 279@LB@Position - sRNA 57 -- 64@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 57 -- 63@LB@
172	0.03064	0.5559	b1542	ydfI	-13.08	0.030437	273 -- 290	69 -- 86	putative NAD-dependent D-mannonate oxidoreductase	_____________272________________291\n_____________\|__________________\|\n5'-CUC...GAAUU______UUA_________GCAUU...ACC-3'\n______________GUUCAU___GGCUUUGGU\n______________\|\|\|\|\|:___\|\|\|\|\|\|:\|\|\n______________CAAGUG___CCGAAAUCA\n3'-CGC...GUUUU______CAA_________AUAAG...AAG-5'\n_____________\|__________________\|\n_____________87_________________68\n	284 -- 290	69 -- 75	-19.6529 kcal/mol	6.00837 kcal/mol	0.568509 kcal/mol	272 291@LB@ \| \|@LB@5'-CUC...GAAUU UUA GCAUU...ACC-3'@LB@ GUUCAU GGCUUUGGU@LB@ \|\|\|\|\|: \|\|\|\|\|\|:\|\|@LB@ CAAGUG CCGAAAUCA@LB@3'-CGC...GUUUU CAA AUAAG...AAG-5'@LB@ \| \|@LB@ 87 68@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -19.6529 kcal/mol@LB@Unfolding Energy - mRNA 6.00837 kcal/mol@LB@Unfolding Energy - sRNA 0.568509 kcal/mol@LB@@LB@Position - mRNA 273 -- 290@LB@Position - sRNA 69 -- 86@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@LB@
44	0.009138	0.5385	b4148	sugE	-12.73	0.035076	273 -- 288	62 -- 77	multidrug efflux system protein	_____________272______________289\n_____________\|________________\|\n5'-CGC...CCCAC_________C______CGCCG...UUA-3'\n______________GGCUUUAGU_GUUUGA\n______________\|\|\|\|\|\|\|\|\|_:\|\|:\|\|\n______________CCGAAAUCA_UAAGCU\n3'-CGC...UGCAA_________A______CAACU...AAG-5'\n_____________\|________________\|\n_____________78_______________61\n	275 -- 281	69 -- 75	-18.0703 kcal/mol	4.60455 kcal/mol	0.736118 kcal/mol	272 289@LB@ \| \|@LB@5'-CGC...CCCAC C CGCCG...UUA-3'@LB@ GGCUUUAGU GUUUGA@LB@ \|\|\|\|\|\|\|\|\| :\|\|:\|\|@LB@ CCGAAAUCA UAAGCU@LB@3'-CGC...UGCAA A CAACU...AAG-5'@LB@ \| \|@LB@ 78 61@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -18.0703 kcal/mol@LB@Unfolding Energy - mRNA 4.60455 kcal/mol@LB@Unfolding Energy - sRNA 0.736118 kcal/mol@LB@@LB@Position - mRNA 273 -- 288@LB@Position - sRNA 62 -- 77@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 69 -- 75@LB@
56	0.01109	0.5385	b0425	panE	-9.95	0.107741	273 -- 289	74 -- 89	2-dehydropantoate reductase NADPH-specific	_____________272_______________290\n_____________\|_________________\|\n5'-AUC...GUCAU________G_GC_____GCGCG...CGC-3'\n______________GAAGUUCA_G__UGGCU\n______________:\|\|\|\|\|\|\|_\|__\|\|\|\|\|\n______________UUUCAAGU_C__ACCGA\n3'-CGC...GGCGU________G_A______AAUCA...AAG-5'\n_____________\|_________________\|\n_____________90________________73\n	274 -- 280	82 -- 88	-18.2046 kcal/mol	7.73441 kcal/mol	0.517373 kcal/mol	272 290@LB@ \| \|@LB@5'-AUC...GUCAU G GC GCGCG...CGC-3'@LB@ GAAGUUCA G UGGCU@LB@ :\|\|\|\|\|\|\| \| \|\|\|\|\|@LB@ UUUCAAGU C ACCGA@LB@3'-CGC...GGCGU G A AAUCA...AAG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -9.95 kcal/mol@LB@Hybridization Energy -18.2046 kcal/mol@LB@Unfolding Energy - mRNA 7.73441 kcal/mol@LB@Unfolding Energy - sRNA 0.517373 kcal/mol@LB@@LB@Position - mRNA 273 -- 289@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 82 -- 88@LB@
181	0.03179	0.5559	b3240	aaeB	-9.50	0.128739	275 -- 287	72 -- 86	p-hydroxybenzoic acid efflux system component	_____________274_____________288\n_____________\|_______________\|\n5'-ACU...GCGCU_______________CACUU...UGG-3'\n______________GUUU__GUUGGCUUU\n______________\|\|\|:__\|\|\|\|\|\|\|\|\|\n______________CAAG__CAACCGAAA\n3'-CGC...GUUUU____UG_________UCAAU...AAG-5'\n_____________\|_______________\|\n_____________87______________71\n	281 -- 287	72 -- 78	-13.8127 kcal/mol	3.79774 kcal/mol	0.514266 kcal/mol	274 288@LB@ \| \|@LB@5'-ACU...GCGCU CACUU...UGG-3'@LB@ GUUU GUUGGCUUU@LB@ \|\|\|: \|\|\|\|\|\|\|\|\|@LB@ CAAG CAACCGAAA@LB@3'-CGC...GUUUU UG UCAAU...AAG-5'@LB@ \| \|@LB@ 87 71@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -13.8127 kcal/mol@LB@Unfolding Energy - mRNA 3.79774 kcal/mol@LB@Unfolding Energy - sRNA 0.514266 kcal/mol@LB@@LB@Position - mRNA 275 -- 287@LB@Position - sRNA 72 -- 86@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 72 -- 78@LB@
43	0.009109	0.5385	b2531	iscR	-9.39	0.134324	275 -- 298	62 -- 87	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________274________________________299\n_____________\|__________________________\|\n5'-AUG...GGCCC___A__________GAUAUUUC____AC-3'\n______________GGU_C_CGUUGGCU_________CGA\n______________:\|\|_\|_\|\|\|\|\|\|\|\|_________\|\|\|\n______________UCA_G_GCAACCGA_________GCU\n3'-CGC...CGUUU___A_U________AAUCAAUAA___CAACU...AAG-5'\n_____________\|__________________________\|\n_____________88_________________________61\n	281 -- 287	74 -- 80	-16.3089 kcal/mol	5.20915 kcal/mol	1.70771 kcal/mol	274 299@LB@ \| \|@LB@5'-AUG...GGCCC A GAUAUUUC AC-3'@LB@ GGU C CGUUGGCU CGA@LB@ :\|\| \| \|\|\|\|\|\|\|\| \|\|\|@LB@ UCA G GCAACCGA GCU@LB@3'-CGC...CGUUU A U AAUCAAUAA CAACU...AAG-5'@LB@ \| \|@LB@ 88 61@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -16.3089 kcal/mol@LB@Unfolding Energy - mRNA 5.20915 kcal/mol@LB@Unfolding Energy - sRNA 1.70771 kcal/mol@LB@@LB@Position - mRNA 275 -- 298@LB@Position - sRNA 62 -- 87@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 74 -- 80@LB@
163	0.02879	0.5559	b4244	pyrI	-5.82	0.477897	276 -- 293	60 -- 77	aspartate carbamoyltransferase regulatory subunit	_____________275________________294\n_____________\|__________________\|\n5'-UUC...AGAUC_______AGCUG______CUGUUCA-3'\n______________GGUUUUA_____UUGAGU\n______________\|\|:\|\|\|\|_____\|:\|\|\|\|\n______________CCGAAAU_____AGCUCA\n3'-CGC...UGCAA_______CAAUA______ACUCU...AAG-5'\n_____________\|__________________\|\n_____________78_________________59\n	276 -- 282	71 -- 77	-12.7499 kcal/mol	6.13118 kcal/mol	0.796465 kcal/mol	275 294@LB@ \| \|@LB@5'-UUC...AGAUC AGCUG CUGUUCA-3'@LB@ GGUUUUA UUGAGU@LB@ \|\|:\|\|\|\| \|:\|\|\|\|@LB@ CCGAAAU AGCUCA@LB@3'-CGC...UGCAA CAAUA ACUCU...AAG-5'@LB@ \| \|@LB@ 78 59@LB@@LB@@LB@Energy -5.82 kcal/mol@LB@Hybridization Energy -12.7499 kcal/mol@LB@Unfolding Energy - mRNA 6.13118 kcal/mol@LB@Unfolding Energy - sRNA 0.796465 kcal/mol@LB@@LB@Position - mRNA 276 -- 293@LB@Position - sRNA 60 -- 77@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 71 -- 77@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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