Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
181	0.0223	0.4113	b3770	ilvE	-12.64	0.069830	250 -- 281	37 -- 61	branched-chain amino acid aminotransferase	_____________249______________________________282\n_____________\|________________________________\|\n5'-UUU...GGUUC_______AGAC____AG___CAU_________CACGC...GCA-3'\n______________GCUGGGA____GCGA__GUG___GUGAUGUCG\n______________:\|\|\|\|:\|____\|\|:\|__\|\|\|___\|::\|\|\|\|\|\|\n______________UGACCUU____CGUU__CAC___CGUUACAGC\n3'-UUU...CAUUA_______________A____U___________ACGAA...GCG-5'\n_____________\|________________________________\|\n_____________62_______________________________36\n	275 -- 281	37 -- 43	-25.0056 kcal/mol	9.06403 kcal/mol	3.30158 kcal/mol	249 282@LB@ \| \|@LB@5'-UUU...GGUUC AGAC AG CAU CACGC...GCA-3'@LB@ GCUGGGA GCGA GUG GUGAUGUCG@LB@ :\|\|\|\|:\| \|\|:\| \|\|\| \|::\|\|\|\|\|\|@LB@ UGACCUU CGUU CAC CGUUACAGC@LB@3'-UUU...CAUUA A U ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -12.64 kcal/mol@LB@Hybridization Energy -25.0056 kcal/mol@LB@Unfolding Energy - mRNA 9.06403 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 250 -- 281@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 37 -- 43@LB@
182	0.02236	0.4113	b2206	napA	-12.10	0.085901	76 -- 101	42 -- 66	nitrate reductase periplasmic large subunit	_____________75_________________________102\n_____________\|__________________________\|\n5'-GAC...UGAUU______G_________AAGAC_____AACGC...UUG-3'\n______________GUGGUG_UGGAAGCAG_____AGCGA\n______________\|\|::\|:_\|\|\|\|\|\|\|\|:_____\|\|\|:\|\n______________CAUUAU_ACCUUCGUU_____UCGUU\n3'-UUU...CGAUU______G_________ACAC______ACAGC...GCG-5'\n_____________\|__________________________\|\n_____________67_________________________41\n	85 -- 91	51 -- 57	-24.6932 kcal/mol	9.28668 kcal/mol	3.30477 kcal/mol	75 102@LB@ \| \|@LB@5'-GAC...UGAUU G AAGAC AACGC...UUG-3'@LB@ GUGGUG UGGAAGCAG AGCGA@LB@ \|\|::\|: \|\|\|\|\|\|\|\|: \|\|\|:\|@LB@ CAUUAU ACCUUCGUU UCGUU@LB@3'-UUU...CGAUU G ACAC ACAGC...GCG-5'@LB@ \| \|@LB@ 67 41@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -24.6932 kcal/mol@LB@Unfolding Energy - mRNA 9.28668 kcal/mol@LB@Unfolding Energy - sRNA 3.30477 kcal/mol@LB@@LB@Position - mRNA 76 -- 101@LB@Position - sRNA 42 -- 66@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 51 -- 57@LB@
183	0.02251	0.4113	b4067	actP	-16.98	0.012652	22 -- 44	66 -- 86	acetate transporter	_____________21______________________45\n_____________\|_______________________\|\n5'-AUC...UGAUC___UUC_________________CACGC...GGC-3'\n______________GCC___GCGCCCGGCUGGCUGGG\n______________\|\|\|___\|\|:\|\|\|\|\|\|\|\|\|\|\|::\|\n______________CGG___CGUGGGCCGACCGAUUC\n_______3'-UUUU___U___________________AUUAU...GCG-5'\n_____________\|_______________________\|\n_____________87______________________65\n	38 -- 44	66 -- 72	-41.8503 kcal/mol	13.121 kcal/mol	11.7541 kcal/mol	21 45@LB@ \| \|@LB@5'-AUC...UGAUC UUC CACGC...GGC-3'@LB@ GCC GCGCCCGGCUGGCUGGG@LB@ \|\|\| \|\|:\|\|\|\|\|\|\|\|\|\|\|::\|@LB@ CGG CGUGGGCCGACCGAUUC@LB@ 3'-UUUU U AUUAU...GCG-5'@LB@ \| \|@LB@ 87 65@LB@@LB@@LB@Energy -16.98 kcal/mol@LB@Hybridization Energy -41.8503 kcal/mol@LB@Unfolding Energy - mRNA 13.121 kcal/mol@LB@Unfolding Energy - sRNA 11.7541 kcal/mol@LB@@LB@Position - mRNA 22 -- 44@LB@Position - sRNA 66 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 66 -- 72@LB@
184	0.02284	0.4113	b2512	bamB	-14.63	0.032048	112 -- 136	38 -- 58	BamABCDE complex OM biogenesis lipoprotein	_____________111_______________________137\n_____________\|_________________________\|\n5'-GCU...GCAUG________GC____AAA________ACUCC...CCC-3'\n______________GGAAGCAG__GUGA___GCGAUGUU\n______________\|\|\|\|\|\|\|:__\|\|\|\|___\|\|:\|\|\|\|:\n______________CCUUCGUU__CACU___CGUUACAG\n3'-UUU...UAUGA________A________________CACGA...GCG-5'\n_____________\|_________________________\|\n_____________59________________________37\n	130 -- 136	38 -- 44	-25.7462 kcal/mol	7.89766 kcal/mol	3.21639 kcal/mol	111 137@LB@ \| \|@LB@5'-GCU...GCAUG GC AAA ACUCC...CCC-3'@LB@ GGAAGCAG GUGA GCGAUGUU@LB@ \|\|\|\|\|\|\|: \|\|\|\| \|\|:\|\|\|\|:@LB@ CCUUCGUU CACU CGUUACAG@LB@3'-UUU...UAUGA A CACGA...GCG-5'@LB@ \| \|@LB@ 59 37@LB@@LB@@LB@Energy -14.63 kcal/mol@LB@Hybridization Energy -25.7462 kcal/mol@LB@Unfolding Energy - mRNA 7.89766 kcal/mol@LB@Unfolding Energy - sRNA 3.21639 kcal/mol@LB@@LB@Position - mRNA 112 -- 136@LB@Position - sRNA 38 -- 58@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 38 -- 44@LB@
185	0.02285	0.4113	b0920	elyC	-11.60	0.104081	77 -- 89	66 -- 78	envelope biogenesis factor; DUF218 superfamily protein	_____________76____________90\n_____________\|_____________\|\n5'-UUG...CUCCA_____________ACGUU...GCC-3'\n______________CCGGUUGGCUAAG\n______________\|\|\|\|:\|\|\|\|\|\|\|\|\n______________GGCCGACCGAUUC\n3'-UUU...UCGUG_____________AUUAU...GCG-5'\n_____________\|_____________\|\n_____________79____________65\n	83 -- 89	66 -- 72	-24.3939 kcal/mol	5.56302 kcal/mol	7.23276 kcal/mol	76 90@LB@ \| \|@LB@5'-UUG...CUCCA ACGUU...GCC-3'@LB@ CCGGUUGGCUAAG@LB@ \|\|\|\|:\|\|\|\|\|\|\|\|@LB@ GGCCGACCGAUUC@LB@3'-UUU...UCGUG AUUAU...GCG-5'@LB@ \| \|@LB@ 79 65@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -24.3939 kcal/mol@LB@Unfolding Energy - mRNA 5.56302 kcal/mol@LB@Unfolding Energy - sRNA 7.23276 kcal/mol@LB@@LB@Position - mRNA 77 -- 89@LB@Position - sRNA 66 -- 78@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 66 -- 72@LB@
186	0.02299	0.4113	b3996	nudC	-11.58	0.104830	175 -- 203	40 -- 67	NADH pyrophosphatase	_____________174____________________________204\n_____________\|______________________________\|\n5'-GAU...AUGCC________AA_________CAA____U___GAUCG...CGG-3'\n______________AGUGAUGC___AGGUAGUG___GAGC_AUG\n______________\|\|\|:\|\|:\|___\|:\|:\|:\|\|___\|\|\|\|_\|\|\|\n______________UCAUUAUG___UUCGUUAC___CUCG_UAC\n3'-UUU...CCGAU________ACC________A______U___AGCAC...GCG-5'\n_____________\|______________________________\|\n_____________68_____________________________39\n	186 -- 192	49 -- 55	-21.6638 kcal/mol	6.77954 kcal/mol	3.30504 kcal/mol	174 204@LB@ \| \|@LB@5'-GAU...AUGCC AA CAA U GAUCG...CGG-3'@LB@ AGUGAUGC AGGUAGUG GAGC AUG@LB@ \|\|\|:\|\|:\| \|:\|:\|:\|\| \|\|\|\| \|\|\|@LB@ UCAUUAUG UUCGUUAC CUCG UAC@LB@3'-UUU...CCGAU ACC A U AGCAC...GCG-5'@LB@ \| \|@LB@ 68 39@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -21.6638 kcal/mol@LB@Unfolding Energy - mRNA 6.77954 kcal/mol@LB@Unfolding Energy - sRNA 3.30504 kcal/mol@LB@@LB@Position - mRNA 175 -- 203@LB@Position - sRNA 40 -- 67@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 49 -- 55@LB@
187	0.023	0.4113	b2311	ubiX	-11.39	0.112499	264 -- 277	17 -- 30	3-octaprenyl-4-hydroxybenzoate carboxy-lyase	_____________263____________278\n_____________\|______________\|\n5'-UGA...UAUUA________G_____UGUCA...AUC-3'\n______________CAGGUUCU_CGCGA\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________GUCCAAGA_GCGCU\n3'-UUU...CGAAA________G_____CCCAG...GCG-5'\n_____________\|______________\|\n_____________31_____________16\n	265 -- 271	23 -- 29	-23.8621 kcal/mol	5.17919 kcal/mol	7.29042 kcal/mol	263 278@LB@ \| \|@LB@5'-UGA...UAUUA G UGUCA...AUC-3'@LB@ CAGGUUCU CGCGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ GUCCAAGA GCGCU@LB@3'-UUU...CGAAA G CCCAG...GCG-5'@LB@ \| \|@LB@ 31 16@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -23.8621 kcal/mol@LB@Unfolding Energy - mRNA 5.17919 kcal/mol@LB@Unfolding Energy - sRNA 7.29042 kcal/mol@LB@@LB@Position - mRNA 264 -- 277@LB@Position - sRNA 17 -- 30@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 23 -- 29@LB@
188	0.02302	0.4113	b3105	yhaJ	-12.66	0.069284	224 -- 245	40 -- 61	LysR family putative transcriptional regulator	_____________223____________________246\n_____________\|______________________\|\n5'-CGG...UUAAC__________CUAC____U___GAUGC...GCG-3'\n______________GCUGGAAGCA____GGGU_AUG\n______________:\|\|\|\|\|\|\|\|\|____\|:\|:_\|\|\|\n______________UGACCUUCGU____CUCG_UAC\n3'-UUU...CAUUA__________UACA____U___AGCAC...GCG-5'\n_____________\|______________________\|\n_____________62_____________________39\n	227 -- 233	52 -- 58	-21.8067 kcal/mol	5.84576 kcal/mol	3.30075 kcal/mol	223 246@LB@ \| \|@LB@5'-CGG...UUAAC CUAC U GAUGC...GCG-3'@LB@ GCUGGAAGCA GGGU AUG@LB@ :\|\|\|\|\|\|\|\|\| \|:\|: \|\|\|@LB@ UGACCUUCGU CUCG UAC@LB@3'-UUU...CAUUA UACA U AGCAC...GCG-5'@LB@ \| \|@LB@ 62 39@LB@@LB@@LB@Energy -12.66 kcal/mol@LB@Hybridization Energy -21.8067 kcal/mol@LB@Unfolding Energy - mRNA 5.84576 kcal/mol@LB@Unfolding Energy - sRNA 3.30075 kcal/mol@LB@@LB@Position - mRNA 224 -- 245@LB@Position - sRNA 40 -- 61@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 52 -- 58@LB@
189	0.02313	0.4113	b2438	eutK	-12.08	0.086588	220 -- 243	37 -- 62	putative ethanol utilization carboxysome structural protein	_____________219________________________244\n_____________\|__________________________\|\n5'-CGA...GGGAU____________AC______UG____CCGCG...GUC-3'\n______________UGCUGGAAGUGG____GGCA__GUCG\n______________\|:\|\|\|\|\|\|\|:::____:\|\|\|__\|\|\|\|\n______________AUGACCUUCGUU____UCGU__CAGC\n3'-UUU...UCAUU____________ACAC____UA____ACGAA...GCG-5'\n_____________\|__________________________\|\n_____________63_________________________36\n	224 -- 230	52 -- 58	-25.7957 kcal/mol	10.4122 kcal/mol	3.3026 kcal/mol	219 244@LB@ \| \|@LB@5'-CGA...GGGAU AC UG CCGCG...GUC-3'@LB@ UGCUGGAAGUGG GGCA GUCG@LB@ \|:\|\|\|\|\|\|\|::: :\|\|\| \|\|\|\|@LB@ AUGACCUUCGUU UCGU CAGC@LB@3'-UUU...UCAUU ACAC UA ACGAA...GCG-5'@LB@ \| \|@LB@ 63 36@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -25.7957 kcal/mol@LB@Unfolding Energy - mRNA 10.4122 kcal/mol@LB@Unfolding Energy - sRNA 3.3026 kcal/mol@LB@@LB@Position - mRNA 220 -- 243@LB@Position - sRNA 37 -- 62@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 52 -- 58@LB@
190	0.02395	0.4226	b1189	dadA	-13.37	0.052568	210 -- 233	43 -- 66	D-amino acid dehydrogenase	_____________209_______________________234\n_____________\|_________________________\|\n5'-CCG...GAGUU__C_____G________________GGCGU...CGG-3'\n______________GU_AUACU_GGAAGUGGUGUG_GUA\n______________\|\|_\|\|\|\|\|_\|\|\|\|\|:::\|\|\|\|_\|:\|\n______________CA_UAUGA_CCUUCGUUACAC_CGU\n3'-UUU...CGAUU__U__________________U___UACAG...GCG-5'\n_____________\|_________________________\|\n_____________67________________________42\n	219 -- 225	52 -- 58	-24.725 kcal/mol	8.04945 kcal/mol	3.30463 kcal/mol	209 234@LB@ \| \|@LB@5'-CCG...GAGUU C G GGCGU...CGG-3'@LB@ GU AUACU GGAAGUGGUGUG GUA@LB@ \|\| \|\|\|\|\| \|\|\|\|\|:::\|\|\|\| \|:\|@LB@ CA UAUGA CCUUCGUUACAC CGU@LB@3'-UUU...CGAUU U U UACAG...GCG-5'@LB@ \| \|@LB@ 67 42@LB@@LB@@LB@Energy -13.37 kcal/mol@LB@Hybridization Energy -24.725 kcal/mol@LB@Unfolding Energy - mRNA 8.04945 kcal/mol@LB@Unfolding Energy - sRNA 3.30463 kcal/mol@LB@@LB@Position - mRNA 210 -- 233@LB@Position - sRNA 43 -- 66@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 52 -- 58@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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