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
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@
47	0.009854	0.5385	b3408	feoA	-10.27	0.095129	159 -- 188	52 -- 83	ferrous iron transporter protein A	_____________158_________________________________189\n_____________\|___________________________________\|\n5'-AGC...CGCCC____A_______________C___UAA________AAGUA...CUG-3'\n______________CAUG__GGU___AGUUA_UC_AGU___UGAGAAAC\n______________\|\|:\|__\|\|:___\|\|\|\|\|_\|\|_\|\|\|___\|\|\|\|\|\|\|\|\n______________GUGC__CCG___UCAAU_AG_UCA___ACUCUUUG\n3'-CGC...UUCAA____AA___AAA_____A__C______________AGAGC...AAG-5'\n_____________\|___________________________________\|\n_____________84__________________________________51\n	182 -- 188	52 -- 58	-20.9255 kcal/mol	6.25891 kcal/mol	4.4004 kcal/mol	158 189@LB@ \| \|@LB@5'-AGC...CGCCC A C UAA AAGUA...CUG-3'@LB@ CAUG GGU AGUUA UC AGU UGAGAAAC@LB@ \|\|:\| \|\|: \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GUGC CCG UCAAU AG UCA ACUCUUUG@LB@3'-CGC...UUCAA AA AAA A C AGAGC...AAG-5'@LB@ \| \|@LB@ 84 51@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -20.9255 kcal/mol@LB@Unfolding Energy - mRNA 6.25891 kcal/mol@LB@Unfolding Energy - sRNA 4.4004 kcal/mol@LB@@LB@Position - mRNA 159 -- 188@LB@Position - sRNA 52 -- 83@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 52 -- 58@LB@
16	0.002981	0.5385	b3428	glgP	-10.45	0.088230	278 -- 289	76 -- 86	glycogen phosphorylase	_____________277__________290\n_____________\|____________\|\n5'-CCA...CUGAU_______A____AAAGG...CGG-3'\n______________GUUUACG_UUGG\n______________\|\|\|:\|\|\|_\|\|\|\|\n______________CAAGUGC_AACC\n3'-CGC...GUUUU____________GAAAU...AAG-5'\n_____________\|____________\|\n_____________87___________75\n	278 -- 284	80 -- 86	-12.981 kcal/mol	2.0211 kcal/mol	0.505081 kcal/mol	277 290@LB@ \| \|@LB@5'-CCA...CUGAU A AAAGG...CGG-3'@LB@ GUUUACG UUGG@LB@ \|\|\|:\|\|\| \|\|\|\|@LB@ CAAGUGC AACC@LB@3'-CGC...GUUUU GAAAU...AAG-5'@LB@ \| \|@LB@ 87 75@LB@@LB@@LB@Energy -10.45 kcal/mol@LB@Hybridization Energy -12.981 kcal/mol@LB@Unfolding Energy - mRNA 2.0211 kcal/mol@LB@Unfolding Energy - sRNA 0.505081 kcal/mol@LB@@LB@Position - mRNA 278 -- 289@LB@Position - sRNA 76 -- 86@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 80 -- 86@LB@
93	0.01594	0.5385	b3430	glgC	-8.76	0.171477	231 -- 238	75 -- 82	glucose-1-phosphate adenylyltransferase	_____________230______239\n_____________\|________\|\n5'-CAG...ACUUA________GCGCC...UGA-3'\n______________AUGUUGGC\n______________\|:\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	232 -- 238	75 -- 81	-11.9398 kcal/mol	2.84031 kcal/mol	0.339284 kcal/mol	230 239@LB@ \| \|@LB@5'-CAG...ACUUA GCGCC...UGA-3'@LB@ AUGUUGGC@LB@ \|:\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.9398 kcal/mol@LB@Unfolding Energy - mRNA 2.84031 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 231 -- 238@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 75 -- 81@LB@
29	0.005218	0.5385	b3433	asd	-11.22	0.064904	208 -- 219	71 -- 82	aspartate-semialdehyde dehydrogenase NAD(P)-binding	_____________207__________220\n_____________\|____________\|\n5'-UCA...GAAAA____________UCGGC...UCU-3'\n______________AUGUUGGUUUUA\n______________\|:\|\|\|\|\|:\|\|\|\|\n______________UGCAACCGAAAU\n3'-CGC...UCAAG____________CAAUA...AAG-5'\n_____________\|____________\|\n_____________83___________70\n	213 -- 219	71 -- 77	-13.9075 kcal/mol	2.30708 kcal/mol	0.38228 kcal/mol	207 220@LB@ \| \|@LB@5'-UCA...GAAAA UCGGC...UCU-3'@LB@ AUGUUGGUUUUA@LB@ \|:\|\|\|\|\|:\|\|\|\|@LB@ UGCAACCGAAAU@LB@3'-CGC...UCAAG CAAUA...AAG-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -13.9075 kcal/mol@LB@Unfolding Energy - mRNA 2.30708 kcal/mol@LB@Unfolding Energy - sRNA 0.38228 kcal/mol@LB@@LB@Position - mRNA 208 -- 219@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 71 -- 77@LB@
102	0.01732	0.5385	b3442	yhhZ	-11.63	0.054951	288 -- 294	75 -- 81	putative Hcp1 family polymorphic toxin protein; putative colicin-like DNase/tRNase activity	_____________287_____295\n_____________\|_______\|\n5'-AUU...GUAAU_______AGAGCG-3'\n______________CGUUGGC\n______________\|\|\|\|\|\|\|\n______________GCAACCG\n3'-CGC...CAAGU_______AAAUC...AAG-5'\n_____________\|_______\|\n_____________82______74\n	288 -- 294	75 -- 81	-12.2648 kcal/mol	0.311297 kcal/mol	0.324493 kcal/mol	287 295@LB@ \| \|@LB@5'-AUU...GUAAU AGAGCG-3'@LB@ CGUUGGC@LB@ \|\|\|\|\|\|\|@LB@ GCAACCG@LB@3'-CGC...CAAGU AAAUC...AAG-5'@LB@ \| \|@LB@ 82 74@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -12.2648 kcal/mol@LB@Unfolding Energy - mRNA 0.311297 kcal/mol@LB@Unfolding Energy - sRNA 0.324493 kcal/mol@LB@@LB@Position - mRNA 288 -- 294@LB@Position - sRNA 75 -- 81@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 75 -- 81@LB@
115	0.01932	0.5385	b3475	acpT	-9.48	0.130030	187 -- 194	75 -- 82	4'-phosphopantetheinyl transferase	_____________186______195\n_____________\|________\|\n5'-GGG...AUUAA________CCUGA...GCU-3'\n______________ACGUUGGC\n______________\|\|\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	188 -- 194	75 -- 81	-13.2305 kcal/mol	3.41608 kcal/mol	0.339284 kcal/mol	186 195@LB@ \| \|@LB@5'-GGG...AUUAA CCUGA...GCU-3'@LB@ ACGUUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -13.2305 kcal/mol@LB@Unfolding Energy - mRNA 3.41608 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 75 -- 81@LB@
166	0.02918	0.5559	b3518	yhjA	-9.21	0.144312	113 -- 127	71 -- 85	putative cytochrome C peroxidase	_____________112_____________128\n_____________\|_______________\|\n5'-CCG...UGUUU______A________UCUCG...GCA-3'\n______________UUUAUG_UGGCUUUG\n______________\|\|:\|:\|_\|\|\|\|\|\|\|:\n______________AAGUGC_ACCGAAAU\n3'-CGC...UUUUC______A________CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	121 -- 127	71 -- 77	-14.7899 kcal/mol	5.0213 kcal/mol	0.560731 kcal/mol	112 128@LB@ \| \|@LB@5'-CCG...UGUUU A UCUCG...GCA-3'@LB@ UUUAUG UGGCUUUG@LB@ \|\|:\|:\| \|\|\|\|\|\|\|:@LB@ AAGUGC ACCGAAAU@LB@3'-CGC...UUUUC A CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -9.21 kcal/mol@LB@Hybridization Energy -14.7899 kcal/mol@LB@Unfolding Energy - mRNA 5.0213 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 113 -- 127@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 71 -- 77@LB@
78	0.01399	0.5385	b3526	kdgK	-7.99	0.228654	189 -- 197	80 -- 88	2-dehydro-3-deoxygluconokinase	_____________188_______198\n_____________\|_________\|\n5'-CCC...AGAUC_________ACUAU...CUU-3'\n______________AGGUUCACG\n______________\|:\|\|\|\|\|\|\|\n______________UUCAAGUGC\n3'-CGC...GCGUU_________AACCG...AAG-5'\n_____________\|_________\|\n_____________89________79\n	191 -- 197	80 -- 86	-11.7911 kcal/mol	3.29177 kcal/mol	0.504555 kcal/mol	188 198@LB@ \| \|@LB@5'-CCC...AGAUC ACUAU...CUU-3'@LB@ AGGUUCACG@LB@ \|:\|\|\|\|\|\|\|@LB@ UUCAAGUGC@LB@3'-CGC...GCGUU AACCG...AAG-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -11.7911 kcal/mol@LB@Unfolding Energy - mRNA 3.29177 kcal/mol@LB@Unfolding Energy - sRNA 0.504555 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 80 -- 86@LB@
82	0.01477	0.5385	b3527	yhjJ	-9.01	0.155560	190 -- 221	62 -- 91	putative periplasmic M16 family chaperone	_____________189_______________________________222\n_____________\|_________________________________\|\n5'-CUC...UUGAU___________AUGCAG___ACAAAA_______CUUUU...GGC-3'\n______________CAGGGGUUCAC______GGC_______AUUCGA\n______________\|\|:::\|\|\|\|\|\|______\|\|\|_______\|\|\|\|\|\|\n______________GUUUUCAAGUG______CCG_______UAAGCU\n3'-CGC...UAGGC___________CAA______AAAUCAA______CAACU...AAG-5'\n_____________\|_________________________________\|\n_____________92________________________________61\n	194 -- 200	81 -- 87	-19.9715 kcal/mol	6.94165 kcal/mol	4.01597 kcal/mol	189 222@LB@ \| \|@LB@5'-CUC...UUGAU AUGCAG ACAAAA CUUUU...GGC-3'@LB@ CAGGGGUUCAC GGC AUUCGA@LB@ \|\|:::\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ GUUUUCAAGUG CCG UAAGCU@LB@3'-CGC...UAGGC CAA AAAUCAA CAACU...AAG-5'@LB@ \| \|@LB@ 92 61@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -19.9715 kcal/mol@LB@Unfolding Energy - mRNA 6.94165 kcal/mol@LB@Unfolding Energy - sRNA 4.01597 kcal/mol@LB@@LB@Position - mRNA 190 -- 221@LB@Position - sRNA 62 -- 91@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 81 -- 87@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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