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
117	0.01966	0.5385	b1203	ychF	-10.24	0.095997	26 -- 41	73 -- 87	catalase inhibitor protein; ATPase K+-dependent ribosome-associated	_____________25_______________42\n_____________\|________________\|\n5'-GAA...AAUGU_______A_A______GACCA...CAU-3'\n______________GGUUUAC_G_UGGCUU\n______________:\|\|\|:\|\|_\|_\|\|\|\|\|\|\n______________UCAAGUG_C_ACCGAA\n3'-CGC...CGUUU_________A______AUCAA...AAG-5'\n_____________\|________________\|\n_____________88_______________72\n	26 -- 32	81 -- 87	-15.1856 kcal/mol	4.42747 kcal/mol	0.51474 kcal/mol	25 42@LB@ \| \|@LB@5'-GAA...AAUGU A A GACCA...CAU-3'@LB@ GGUUUAC G UGGCUU@LB@ :\|\|\|:\|\| \| \|\|\|\|\|\|@LB@ UCAAGUG C ACCGAA@LB@3'-CGC...CGUUU A AUCAA...AAG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -15.1856 kcal/mol@LB@Unfolding Energy - mRNA 4.42747 kcal/mol@LB@Unfolding Energy - sRNA 0.51474 kcal/mol@LB@@LB@Position - mRNA 26 -- 41@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 81 -- 87@LB@
131	0.02244	0.5385	b1713	pheT	-10.81	0.076409	64 -- 80	73 -- 89	phenylalanine tRNA synthetase beta subunit	_____________63________________81\n_____________\|_________________\|\n5'-CUG...ACCCG_________UC______CGCCU...ACG-3'\n______________GAAGUUUAC__UGGUUU\n______________:\|\|\|\|\|:\|\|__\|\|\|:\|\|\n______________UUUCAAGUG__ACCGAA\n3'-CGC...GGCGU_________CA______AUCAA...AAG-5'\n_____________\|_________________\|\n_____________90________________72\n	66 -- 72	81 -- 87	-14.6363 kcal/mol	3.30516 kcal/mol	0.517627 kcal/mol	63 81@LB@ \| \|@LB@5'-CUG...ACCCG UC CGCCU...ACG-3'@LB@ GAAGUUUAC UGGUUU@LB@ :\|\|\|\|\|:\|\| \|\|\|:\|\|@LB@ UUUCAAGUG ACCGAA@LB@3'-CGC...GGCGU CA AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -10.81 kcal/mol@LB@Hybridization Energy -14.6363 kcal/mol@LB@Unfolding Energy - mRNA 3.30516 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 64 -- 80@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 81 -- 87@LB@
171	0.03054	0.5559	b0045	yaaU	-10.82	0.076059	142 -- 153	73 -- 84	putative MFS sugar transporter; membrane protein	_____________141__________154\n_____________\|____________\|\n5'-AAG...ACGGC_G__________GAUAC...UAC-3'\n______________U_AUGUUGGUUU\n______________\|_\|:\|\|\|\|\|:\|\|\n______________A_UGCAACCGAA\n3'-CGC...UUUCA_G__________AUCAA...AAG-5'\n_____________\|____________\|\n_____________85___________72\n	147 -- 153	73 -- 79	-12.9415 kcal/mol	1.60777 kcal/mol	0.508835 kcal/mol	141 154@LB@ \| \|@LB@5'-AAG...ACGGC G GAUAC...UAC-3'@LB@ U AUGUUGGUUU@LB@ \| \|:\|\|\|\|\|:\|\|@LB@ A UGCAACCGAA@LB@3'-CGC...UUUCA G AUCAA...AAG-5'@LB@ \| \|@LB@ 85 72@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -12.9415 kcal/mol@LB@Unfolding Energy - mRNA 1.60777 kcal/mol@LB@Unfolding Energy - sRNA 0.508835 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 73 -- 84@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 73 -- 79@LB@
174	0.03067	0.5559	b4005	purD	-11.17	0.066076	4 -- 22	73 -- 90	phosphoribosylglycinamide synthetase phosphoribosylamine-glycine ligase	_____________3___________________23\n_____________\|___________________\|\n________5'-GUG________CU__A______CUGAC...GUA-3'\n______________AAAGGUUC__CG_UGGCUU\n______________\|\|\|:\|\|\|\|__\|\|_\|\|\|\|\|\|\n______________UUUUCAAG__GC_ACCGAA\n3'-CGC...AGGCG________U___A______AUCAA...AAG-5'\n_____________\|___________________\|\n_____________91__________________72\n	5 -- 11	83 -- 89	-16.9563 kcal/mol	5.26463 kcal/mol	0.517799 kcal/mol	3 23@LB@ \| \|@LB@ 5'-GUG CU A CUGAC...GUA-3'@LB@ AAAGGUUC CG UGGCUU@LB@ \|\|\|:\|\|\|\| \|\| \|\|\|\|\|\|@LB@ UUUUCAAG GC ACCGAA@LB@3'-CGC...AGGCG U A AUCAA...AAG-5'@LB@ \| \|@LB@ 91 72@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -16.9563 kcal/mol@LB@Unfolding Energy - mRNA 5.26463 kcal/mol@LB@Unfolding Energy - sRNA 0.517799 kcal/mol@LB@@LB@Position - mRNA 4 -- 22@LB@Position - sRNA 73 -- 90@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 83 -- 89@LB@
4	0.0006326	0.5173	b3230	rpsI	-11.95	0.048152	221 -- 251	74 -- 108	30S ribosomal subunit protein S9	_____________220_________________________________252\n_____________\|___________________________________\|\n5'-GUG...UACUA___CA_____UCG________________CA____CGCGU...GUU-3'\n______________CGG___CUGG____CCGCAAAAGUUC_CG___GCU\n______________\|\|\|___\|\|\|\|____\|\|\|\|\|\|\|\|\|\|\|\|_\|\|___\|\|\|\n______________GCC___GACC____GGCGUUUUCAAG_GC___CGA\n__________3'-C___UAG____UCUA____________U__AAC___AAUCA...AAG-5'\n_____________\|___________________________________\|\n_____________109_________________________________73\n	238 -- 244	83 -- 89	-33.5849 kcal/mol	9.75151 kcal/mol	11.8795 kcal/mol	220 252@LB@ \| \|@LB@5'-GUG...UACUA CA UCG CA CGCGU...GUU-3'@LB@ CGG CUGG CCGCAAAAGUUC CG GCU@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\| \|\| \|\|\|@LB@ GCC GACC GGCGUUUUCAAG GC CGA@LB@ 3'-C UAG UCUA U AAC AAUCA...AAG-5'@LB@ \| \|@LB@ 109 73@LB@@LB@@LB@Energy -11.95 kcal/mol@LB@Hybridization Energy -33.5849 kcal/mol@LB@Unfolding Energy - mRNA 9.75151 kcal/mol@LB@Unfolding Energy - sRNA 11.8795 kcal/mol@LB@@LB@Position - mRNA 221 -- 251@LB@Position - sRNA 74 -- 108@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 83 -- 89@LB@
48	0.009918	0.5385	b0641	lptE	-9.88	0.110832	177 -- 184	74 -- 81	LPS assembly OM complex LptDE lipoprotein component	_____________176______185\n_____________\|________\|\n5'-ACG...CUGGU________AAGCG...UGA-3'\n______________CGUUGGCU\n______________\|\|\|\|\|\|\|\|\n______________GCAACCGA\n3'-CGC...CAAGU________AAUCA...AAG-5'\n_____________\|________\|\n_____________82_______73\n	178 -- 184	74 -- 80	-13.2047 kcal/mol	2.99134 kcal/mol	0.332056 kcal/mol	176 185@LB@ \| \|@LB@5'-ACG...CUGGU AAGCG...UGA-3'@LB@ CGUUGGCU@LB@ \|\|\|\|\|\|\|\|@LB@ GCAACCGA@LB@3'-CGC...CAAGU AAUCA...AAG-5'@LB@ \| \|@LB@ 82 73@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -13.2047 kcal/mol@LB@Unfolding Energy - mRNA 2.99134 kcal/mol@LB@Unfolding Energy - sRNA 0.332056 kcal/mol@LB@@LB@Position - mRNA 177 -- 184@LB@Position - sRNA 74 -- 81@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 74 -- 80@LB@
50	0.0104	0.5385	b0661	miaB	-10.15	0.099644	35 -- 45	74 -- 85	tRNA-i(6)A37 methylthiotransferase	_____________34___________46\n_____________\|____________\|\n5'-CGC...GCAAU____________GAUUU...AAC-3'\n______________UUC_CGUUGGUU\n______________\|\|\|_\|\|\|\|\|\|:\|\n______________AAG_GCAACCGA\n3'-CGC...UUUUC___U________AAUCA...AAG-5'\n_____________\|____________\|\n_____________86___________73\n	39 -- 45	74 -- 80	-13.4892 kcal/mol	2.82751 kcal/mol	0.512001 kcal/mol	34 46@LB@ \| \|@LB@5'-CGC...GCAAU GAUUU...AAC-3'@LB@ UUC CGUUGGUU@LB@ \|\|\| \|\|\|\|\|\|:\|@LB@ AAG GCAACCGA@LB@3'-CGC...UUUUC U AAUCA...AAG-5'@LB@ \| \|@LB@ 86 73@LB@@LB@@LB@Energy -10.15 kcal/mol@LB@Hybridization Energy -13.4892 kcal/mol@LB@Unfolding Energy - mRNA 2.82751 kcal/mol@LB@Unfolding Energy - sRNA 0.512001 kcal/mol@LB@@LB@Position - mRNA 35 -- 45@LB@Position - sRNA 74 -- 85@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 74 -- 80@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@
57	0.01133	0.5385	b0026	ileS	-8.45	0.192830	289 -- 299	74 -- 83	isoleucyl-tRNA synthetase	_____________288_________300\n_____________\|___________\|\n5'-AUG...GCUGG________A__G-3'\n______________CGCGUUGG_CU\n______________\|:\|\|\|\|\|\|_\|\|\n______________GUGCAACC_GA\n3'-CGC...UUCAA___________AAUCA...AAG-5'\n_____________\|___________\|\n_____________84__________73\n	290 -- 296	76 -- 82	-13.1796 kcal/mol	4.23376 kcal/mol	0.494551 kcal/mol	288 300@LB@ \| \|@LB@5'-AUG...GCUGG A G-3'@LB@ CGCGUUGG CU@LB@ \|:\|\|\|\|\|\| \|\|@LB@ GUGCAACC GA@LB@3'-CGC...UUCAA AAUCA...AAG-5'@LB@ \| \|@LB@ 84 73@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -13.1796 kcal/mol@LB@Unfolding Energy - mRNA 4.23376 kcal/mol@LB@Unfolding Energy - sRNA 0.494551 kcal/mol@LB@@LB@Position - mRNA 289 -- 299@LB@Position - sRNA 74 -- 83@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 76 -- 82@LB@
59	0.01163	0.5385	b1279	yciS	-7.12	0.313424	44 -- 60	74 -- 90	DUF1049 family inner membrane protein function unknown	_____________43________________61\n_____________\|_________________\|\n5'-ACC...AACAA_______A___C_____GAUUU...UGU-3'\n______________GAAAGUU_ACG_UGGUU\n______________:\|\|\|\|\|\|_\|\|\|_\|\|\|:\|\n______________UUUUCAA_UGC_ACCGA\n3'-CGC...AGGCG_______G___A_____AAUCA...AAG-5'\n_____________\|_________________\|\n_____________91________________73\n	44 -- 50	84 -- 90	-13.3715 kcal/mol	5.7376 kcal/mol	0.517587 kcal/mol	43 61@LB@ \| \|@LB@5'-ACC...AACAA A C GAUUU...UGU-3'@LB@ GAAAGUU ACG UGGUU@LB@ :\|\|\|\|\|\| \|\|\| \|\|\|:\|@LB@ UUUUCAA UGC ACCGA@LB@3'-CGC...AGGCG G A AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -7.12 kcal/mol@LB@Hybridization Energy -13.3715 kcal/mol@LB@Unfolding Energy - mRNA 5.7376 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 44 -- 60@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 84 -- 90@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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