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
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@
170	0.03041	0.5559	b1629	rsxC	-10.04	0.103937	197 -- 215	64 -- 83	SoxR iron-sulfur cluster reduction factor component; putative membrane-associated NADH oxidoreductase of electron transport complex	_____________196__________________216\n_____________\|____________________\|\n5'-UCA...UGGAA___CAU_____A________UCUGC...CCC-3'\n______________CAC____GCUU_AGUUAUUC\n______________\|\|\|____\|\|\|\|_\|\|\|\|\|\|\|\|\n______________GUG____CGAA_UCAAUAAG\n3'-CGC...UUCAA___CAAC____A________CUCAA...AAG-5'\n_____________\|____________________\|\n_____________84___________________63\n	209 -- 215	64 -- 70	-13.7112 kcal/mol	3.10702 kcal/mol	0.560651 kcal/mol	196 216@LB@ \| \|@LB@5'-UCA...UGGAA CAU A UCUGC...CCC-3'@LB@ CAC GCUU AGUUAUUC@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUG CGAA UCAAUAAG@LB@3'-CGC...UUCAA CAAC A CUCAA...AAG-5'@LB@ \| \|@LB@ 84 63@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -13.7112 kcal/mol@LB@Unfolding Energy - mRNA 3.10702 kcal/mol@LB@Unfolding Energy - sRNA 0.560651 kcal/mol@LB@@LB@Position - mRNA 197 -- 215@LB@Position - sRNA 64 -- 83@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 64 -- 70@LB@
150	0.02548	0.5485	b0180	fabZ	-10.02	0.104939	240 -- 263	1 -- 24	(3R)-hydroxymyristol acyl carrier protein dehydratase	_____________239______________________264\n_____________\|________________________\|\n5'-AAA...AGAUU______CUUC______A_______CCGUU...AAG-3'\n______________UUAGAA____UGCCGC_CCGUUUC\n______________\|\|\|:\|\|____\|\|\|\|\|\|_\|\|\|\|\|\|\|\n______________AAUUUU____ACGGCG_GGCAAAG\n3'-CGC...UUCCC______CUCC______A_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	257 -- 263	1 -- 7	-23.7452 kcal/mol	3.39044 kcal/mol	10.3355 kcal/mol	239 264@LB@ \| \|@LB@5'-AAA...AGAUU CUUC A CCGUU...AAG-3'@LB@ UUAGAA UGCCGC CCGUUUC@LB@ \|\|\|:\|\| \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAUUUU ACGGCG GGCAAAG@LB@3'-CGC...UUCCC CUCC A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -23.7452 kcal/mol@LB@Unfolding Energy - mRNA 3.39044 kcal/mol@LB@Unfolding Energy - sRNA 10.3355 kcal/mol@LB@@LB@Position - mRNA 240 -- 263@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 1 -- 7@LB@
125	0.02168	0.5385	b3380	yhfW	-9.99	0.106098	159 -- 190	48 -- 81	phosphopentomutase-related metalloenzyme superfamily protein	_____________158_________________________________191\n_____________\|___________________________________\|\n5'-CUC...GAAAU___C___C________GAC___CUU__________UGGGG...GUG-3'\n______________CGU_GGU____GUUAU___AGU___GGAAACUCUC\n______________\|\|\|_\|\|:____\|\|\|\|\|___\|\|\|___:\|\|\|\|\|\|\|\|\|\n______________GCA_CCG____CAAUA___UCA___UCUUUGAGAG\n3'-CGC...CAAGU___A___AAAU_____AGC___AC___________CUUUG...AAG-5'\n_____________\|___________________________________\|\n_____________82__________________________________47\n	184 -- 190	48 -- 54	-22.1995 kcal/mol	7.79728 kcal/mol	4.41067 kcal/mol	158 191@LB@ \| \|@LB@5'-CUC...GAAAU C C GAC CUU UGGGG...GUG-3'@LB@ CGU GGU GUUAU AGU GGAAACUCUC@LB@ \|\|\| \|\|: \|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|\|\|@LB@ GCA CCG CAAUA UCA UCUUUGAGAG@LB@3'-CGC...CAAGU A AAAU AGC AC CUUUG...AAG-5'@LB@ \| \|@LB@ 82 47@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -22.1995 kcal/mol@LB@Unfolding Energy - mRNA 7.79728 kcal/mol@LB@Unfolding Energy - sRNA 4.41067 kcal/mol@LB@@LB@Position - mRNA 159 -- 190@LB@Position - sRNA 48 -- 81@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 48 -- 54@LB@
180	0.03162	0.5559	b1941	fliI	-9.97	0.106944	57 -- 70	74 -- 88	flagellum-specific ATP synthase	_____________56______________71\n_____________\|_______________\|\n5'-CUG...ACCUU________A______GGCGC...GCG-3'\n______________AAGUUUGC__UGGCU\n______________\|\|\|\|\|::\|__\|\|\|\|\|\n______________UUCAAGUG__ACCGA\n3'-CGC...GCGUU________CA_____AAUCA...AAG-5'\n_____________\|_______________\|\n_____________89______________73\n	58 -- 64	81 -- 87	-13.0478 kcal/mol	2.55971 kcal/mol	0.516514 kcal/mol	56 71@LB@ \| \|@LB@5'-CUG...ACCUU A GGCGC...GCG-3'@LB@ AAGUUUGC UGGCU@LB@ \|\|\|\|\|::\| \|\|\|\|\|@LB@ UUCAAGUG ACCGA@LB@3'-CGC...GCGUU CA AAUCA...AAG-5'@LB@ \| \|@LB@ 89 73@LB@@LB@@LB@Energy -9.97 kcal/mol@LB@Hybridization Energy -13.0478 kcal/mol@LB@Unfolding Energy - mRNA 2.55971 kcal/mol@LB@Unfolding Energy - sRNA 0.516514 kcal/mol@LB@@LB@Position - mRNA 57 -- 70@LB@Position - sRNA 74 -- 88@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 81 -- 87@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@
197	0.0346	0.5559	b2829	ptsP	-9.94	0.108120	103 -- 113	80 -- 90	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	_____________102_________114\n_____________\|___________\|\n5'-CCA...AAUGA___________AGUGU...UGG-3'\n______________AAGAGUUCGCG\n______________\|\|:\|\|\|\|\|:\|\|\n______________UUUUCAAGUGC\n3'-CGC...AGGCG___________AACCG...AAG-5'\n_____________\|___________\|\n_____________91__________79\n	107 -- 113	80 -- 86	-13.2227 kcal/mol	2.77203 kcal/mol	0.506776 kcal/mol	102 114@LB@ \| \|@LB@5'-CCA...AAUGA AGUGU...UGG-3'@LB@ AAGAGUUCGCG@LB@ \|\|:\|\|\|\|\|:\|\|@LB@ UUUUCAAGUGC@LB@3'-CGC...AGGCG AACCG...AAG-5'@LB@ \| \|@LB@ 91 79@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -13.2227 kcal/mol@LB@Unfolding Energy - mRNA 2.77203 kcal/mol@LB@Unfolding Energy - sRNA 0.506776 kcal/mol@LB@@LB@Position - mRNA 103 -- 113@LB@Position - sRNA 80 -- 90@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 80 -- 86@LB@
126	0.02177	0.5385	b4162	orn	-9.93	0.108535	62 -- 89	61 -- 86	oligoribonuclease	_____________61___________________________90\n_____________\|____________________________\|\n5'-ACA...UUGGC_______CG_C___GC___CCU__G___AGUUU...CCG-3'\n______________GUUCACG__G_GCU__UGG___UU_GAG\n______________\|\|\|\|\|\|\|__\|_\|\|\|__\|:\|___\|\|_\|\|\|\n______________CAAGUGC__C_CGA__AUC___AA_CUC\n3'-CGC...GUUUU_______AA_____A____AAU__G___AACUC...AAG-5'\n_____________\|____________________________\|\n_____________87___________________________60\n	62 -- 68	80 -- 86	-20.598 kcal/mol	8.95458 kcal/mol	1.70915 kcal/mol	61 90@LB@ \| \|@LB@5'-ACA...UUGGC CG C GC CCU G AGUUU...CCG-3'@LB@ GUUCACG G GCU UGG UU GAG@LB@ \|\|\|\|\|\|\| \| \|\|\| \|:\| \|\| \|\|\|@LB@ CAAGUGC C CGA AUC AA CUC@LB@3'-CGC...GUUUU AA A AAU G AACUC...AAG-5'@LB@ \| \|@LB@ 87 60@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -20.598 kcal/mol@LB@Unfolding Energy - mRNA 8.95458 kcal/mol@LB@Unfolding Energy - sRNA 1.70915 kcal/mol@LB@@LB@Position - mRNA 62 -- 89@LB@Position - sRNA 61 -- 86@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 80 -- 86@LB@
84	0.01516	0.5385	b1871	cmoB	-9.91	0.109770	166 -- 183	71 -- 87	tRNA (cmo5U34)-carboxymethyltransferase carboxy-SAM-dependent	_____________165________________184\n_____________\|__________________\|\n5'-CAC...ACUUU_______U_G____A___AAAGC...AGC-3'\n______________GGUUCAC_G_UGGC_UUA\n______________:\|\|\|\|\|\|_\|_\|\|\|\|_\|\|\|\n______________UCAAGUG_C_ACCG_AAU\n3'-CGC...CGUUU_________A____A___CAAUA...AAG-5'\n_____________\|__________________\|\n_____________88_________________70\n	166 -- 172	81 -- 87	-14.4863 kcal/mol	4.01825 kcal/mol	0.562376 kcal/mol	165 184@LB@ \| \|@LB@5'-CAC...ACUUU U G A AAAGC...AGC-3'@LB@ GGUUCAC G UGGC UUA@LB@ :\|\|\|\|\|\| \| \|\|\|\| \|\|\|@LB@ UCAAGUG C ACCG AAU@LB@3'-CGC...CGUUU A A CAAUA...AAG-5'@LB@ \| \|@LB@ 88 70@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -14.4863 kcal/mol@LB@Unfolding Energy - mRNA 4.01825 kcal/mol@LB@Unfolding Energy - sRNA 0.562376 kcal/mol@LB@@LB@Position - mRNA 166 -- 183@LB@Position - sRNA 71 -- 87@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 81 -- 87@LB@
106	0.01861	0.5385	b2754	ygbF	-9.88	0.110684	283 -- 300	13 -- 30	CRISPR adaptation ssRNA endonuclease	_____________282_______________300\n_____________\|_________________\|\n5'-UGG...ACGUG_______AUAUGU_____-3'\n______________CAGGGGU______AGGUG\n______________\|\|:\|\|\|\|______\|\|\|\|\|\n______________GUUCCCA______UCCAC\n3'-CGC...CUGAA_______AUUUUC_____GGCGA...AAG-5'\n_____________\|__________________\|\n_____________31_________________12\n	283 -- 289	24 -- 30	-16.4011 kcal/mol	3.18452 kcal/mol	3.3319 kcal/mol	282 300@LB@ \| \|@LB@5'-UGG...ACGUG AUAUGU -3'@LB@ CAGGGGU AGGUG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ GUUCCCA UCCAC@LB@3'-CGC...CUGAA AUUUUC GGCGA...AAG-5'@LB@ \| \|@LB@ 31 12@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -16.4011 kcal/mol@LB@Unfolding Energy - mRNA 3.18452 kcal/mol@LB@Unfolding Energy - sRNA 3.3319 kcal/mol@LB@@LB@Position - mRNA 283 -- 300@LB@Position - sRNA 13 -- 30@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 24 -- 30@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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