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
143	0.02402	0.5467	b4029	yjbH	-10.20	0.097639	107 -- 117	75 -- 85	DUF940 family extracellular polysaccharide protein	_____________106_________118\n_____________\|___________\|\n5'-GCG...CAUUA___________CUCGC...AUU-3'\n______________UUUAUGUUGGC\n______________\|\|:\|:\|\|\|\|\|\|\n______________AAGUGCAACCG\n3'-CGC...UUUUC___________AAAUC...AAG-5'\n_____________\|___________\|\n_____________86__________74\n	111 -- 117	75 -- 81	-14.6823 kcal/mol	3.97178 kcal/mol	0.509769 kcal/mol	106 118@LB@ \| \|@LB@5'-GCG...CAUUA CUCGC...AUU-3'@LB@ UUUAUGUUGGC@LB@ \|\|:\|:\|\|\|\|\|\|@LB@ AAGUGCAACCG@LB@3'-CGC...UUUUC AAAUC...AAG-5'@LB@ \| \|@LB@ 86 74@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -14.6823 kcal/mol@LB@Unfolding Energy - mRNA 3.97178 kcal/mol@LB@Unfolding Energy - sRNA 0.509769 kcal/mol@LB@@LB@Position - mRNA 107 -- 117@LB@Position - sRNA 75 -- 85@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 75 -- 81@LB@
80	0.01445	0.5385	b4257	yjgN	-10.51	0.086376	202 -- 215	65 -- 78	DUF898 family inner membrane protein	_____________201____________216\n_____________\|______________\|\n5'-UUA...UUUUA_____CA_______AAUGA...UGU-3'\n______________UGGCU__AGUUAUU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\n______________ACCGA__UCAAUAA\n3'-CGC...GUGCA_____AA_______GCUCA...AAG-5'\n_____________\|______________\|\n_____________79_____________64\n	209 -- 215	65 -- 71	-13.5706 kcal/mol	2.80573 kcal/mol	0.256929 kcal/mol	201 216@LB@ \| \|@LB@5'-UUA...UUUUA CA AAUGA...UGU-3'@LB@ UGGCU AGUUAUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ ACCGA UCAAUAA@LB@3'-CGC...GUGCA AA GCUCA...AAG-5'@LB@ \| \|@LB@ 79 64@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -13.5706 kcal/mol@LB@Unfolding Energy - mRNA 2.80573 kcal/mol@LB@Unfolding Energy - sRNA 0.256929 kcal/mol@LB@@LB@Position - mRNA 202 -- 215@LB@Position - sRNA 65 -- 78@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 65 -- 71@LB@
130	0.02238	0.5385	b4365	yjjQ	-17.31	0.005324	260 -- 274	14 -- 28	putative transcriptional regulator	_____________259_____________275\n_____________\|_______________\|\n5'-AGG...CAAGC_______________CAUGA...AUG-3'\n______________AGGGUUAAAAGAGGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UCCCAAUUUUCUCCA\n3'-CGC...GAAGU_______________CGGCG...AAG-5'\n_____________\|_______________\|\n_____________29______________13\n	268 -- 274	14 -- 20	-23.2971 kcal/mol	2.73817 kcal/mol	3.24497 kcal/mol	259 275@LB@ \| \|@LB@5'-AGG...CAAGC CAUGA...AUG-3'@LB@ AGGGUUAAAAGAGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UCCCAAUUUUCUCCA@LB@3'-CGC...GAAGU CGGCG...AAG-5'@LB@ \| \|@LB@ 29 13@LB@@LB@@LB@Energy -17.31 kcal/mol@LB@Hybridization Energy -23.2971 kcal/mol@LB@Unfolding Energy - mRNA 2.73817 kcal/mol@LB@Unfolding Energy - sRNA 3.24497 kcal/mol@LB@@LB@Position - mRNA 260 -- 274@LB@Position - sRNA 14 -- 28@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 14 -- 20@LB@
54	0.01077	0.5385	b1820	yobD	-10.70	0.079862	85 -- 97	73 -- 84	UPF0266 family inner membrane protein	_____________84____________98\n_____________\|_____________\|\n5'-ACC...GUGGA___U_________CUUCG...CCC-3'\n______________UCA_CGUUGGCUU\n______________\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AGU_GCAACCGAA\n3'-CGC...UUUCA_____________AUCAA...AAG-5'\n_____________\|_____________\|\n_____________85____________72\n	91 -- 97	73 -- 79	-16.3135 kcal/mol	5.10116 kcal/mol	0.508835 kcal/mol	84 98@LB@ \| \|@LB@5'-ACC...GUGGA U CUUCG...CCC-3'@LB@ UCA CGUUGGCUU@LB@ \|\|\| \|\|\|\|\|\|\|\|\|@LB@ AGU GCAACCGAA@LB@3'-CGC...UUUCA AUCAA...AAG-5'@LB@ \| \|@LB@ 85 72@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -16.3135 kcal/mol@LB@Unfolding Energy - mRNA 5.10116 kcal/mol@LB@Unfolding Energy - sRNA 0.508835 kcal/mol@LB@@LB@Position - mRNA 85 -- 97@LB@Position - sRNA 73 -- 84@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 73 -- 79@LB@
18	0.003137	0.5385	b1824	yobF	-13.30	0.027752	169 -- 188	14 -- 35	DUF2527 family heat-induced protein	_____________168____________________189\n_____________\|______________________\|\n5'-GCC...UAACA________________C_____ACAGU...UGU-3'\n______________GAUUUC__GGGUUAAA_GAGGU\n______________\|\|:\|\|\|__\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUGAAG__CCCAAUUU_CUCCA\n3'-CGC...CGUCA______UU________U_____CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	176 -- 182	20 -- 26	-23.4961 kcal/mol	6.86312 kcal/mol	3.33183 kcal/mol	168 189@LB@ \| \|@LB@5'-GCC...UAACA C ACAGU...UGU-3'@LB@ GAUUUC GGGUUAAA GAGGU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUGAAG CCCAAUUU CUCCA@LB@3'-CGC...CGUCA UU U CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -13.30 kcal/mol@LB@Hybridization Energy -23.4961 kcal/mol@LB@Unfolding Energy - mRNA 6.86312 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 169 -- 188@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 20 -- 26@LB@
26	0.00484	0.5385	b3033	yqiB	-11.20	0.065436	106 -- 117	15 -- 27	DUF1249 protein YqiB	_____________105___________118\n_____________\|_____________\|\n5'-UGG...CCAGU_____________GGAAA...GCG-3'\n______________GGG_UAGAAGAGG\n______________\|\|\|_\|\|:\|\|\|\|\|\|\n______________CCC_AUUUUCUCC\n3'-CGC...AAGUU___A_________ACGGC...AAG-5'\n_____________\|_____________\|\n_____________28____________14\n	111 -- 117	15 -- 21	-17.3581 kcal/mol	2.92425 kcal/mol	3.23583 kcal/mol	105 118@LB@ \| \|@LB@5'-UGG...CCAGU GGAAA...GCG-3'@LB@ GGG UAGAAGAGG@LB@ \|\|\| \|\|:\|\|\|\|\|\|@LB@ CCC AUUUUCUCC@LB@3'-CGC...AAGUU A ACGGC...AAG-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -17.3581 kcal/mol@LB@Unfolding Energy - mRNA 2.92425 kcal/mol@LB@Unfolding Energy - sRNA 3.23583 kcal/mol@LB@@LB@Position - mRNA 106 -- 117@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 15 -- 21@LB@
165	0.02909	0.5559	b3283	yrdD	-9.69	0.119373	265 -- 285	52 -- 72	ssDNA-binding protein function unknown	_____________264___________________286\n_____________\|_____________________\|\n5'-AAC...UGAAC___________UCC_______ACGGU...UUG-3'\n______________UGGUUAUUCGA___GGGAAAC\n______________\|:\|\|\|\|\|\|\|\|\|___\|:\|\|\|\|\|\n______________AUCAAUAAGCU___CUCUUUG\n3'-CGC...CCGAA___________CAA_______AGAGC...AAG-5'\n_____________\|_____________________\|\n_____________73____________________51\n	279 -- 285	52 -- 58	-20.8466 kcal/mol	6.85358 kcal/mol	4.29991 kcal/mol	264 286@LB@ \| \|@LB@5'-AAC...UGAAC UCC ACGGU...UUG-3'@LB@ UGGUUAUUCGA GGGAAAC@LB@ \|:\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ AUCAAUAAGCU CUCUUUG@LB@3'-CGC...CCGAA CAA AGAGC...AAG-5'@LB@ \| \|@LB@ 73 51@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -20.8466 kcal/mol@LB@Unfolding Energy - mRNA 6.85358 kcal/mol@LB@Unfolding Energy - sRNA 4.29991 kcal/mol@LB@@LB@Position - mRNA 265 -- 285@LB@Position - sRNA 52 -- 72@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 52 -- 58@LB@
94	0.01616	0.5385	b4217	ytfK	-8.94	0.160287	283 -- 290	75 -- 82	DUF1107 family protein	_____________282______291\n_____________\|________\|\n5'-GAA...CAAGG________GCUUU...AAU-3'\n______________ACGUUGGC\n______________\|\|\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	284 -- 290	75 -- 81	-13.4875 kcal/mol	4.21202 kcal/mol	0.339284 kcal/mol	282 291@LB@ \| \|@LB@5'-GAA...CAAGG GCUUU...AAU-3'@LB@ ACGUUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -13.4875 kcal/mol@LB@Unfolding Energy - mRNA 4.21202 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 283 -- 290@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 75 -- 81@LB@
74	0.01362	0.5385	b0946	zapC	-12.02	0.046851	175 -- 197	15 -- 35	FtsZ stabilizer	_____________174_____________________198\n_____________\|_______________________\|\n5'-AUU...GCUGC_______U_____AG________CAGAU...GUU-3'\n______________GGUUUUA_AGGGU__GGGAGAGG\n______________\|::\|\|:\|_\|\|\|\|\|__:::\|\|\|\|\|\n______________CUGAAGU_UCCCA__UUUUCUCC\n3'-CGC...CGUCA_____________A_________ACGGC...AAG-5'\n_____________\|_______________________\|\n_____________36______________________14\n	191 -- 197	15 -- 21	-19.3355 kcal/mol	3.98393 kcal/mol	3.33058 kcal/mol	174 198@LB@ \| \|@LB@5'-AUU...GCUGC U AG CAGAU...GUU-3'@LB@ GGUUUUA AGGGU GGGAGAGG@LB@ \|::\|\|:\| \|\|\|\|\| :::\|\|\|\|\|@LB@ CUGAAGU UCCCA UUUUCUCC@LB@3'-CGC...CGUCA A ACGGC...AAG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -19.3355 kcal/mol@LB@Unfolding Energy - mRNA 3.98393 kcal/mol@LB@Unfolding Energy - sRNA 3.33058 kcal/mol@LB@@LB@Position - mRNA 175 -- 197@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 15 -- 21@LB@
188	0.03339	0.5559	b3232	zapE	-6.91	0.336884	267 -- 282	15 -- 35	divisome ATPase	_____________266____________________283\n_____________\|______________________\|\n5'-AGG...CCGAC___G__________________CCGUC...AAA-3'\n______________GAC_UUCA______AAAAGAGG\n______________\|\|\|_\|\|\|\|______\|\|\|\|\|\|\|\|\n______________CUG_AAGU______UUUUCUCC\n3'-CGC...CGUCA________UCCCAA________ACGGC...AAG-5'\n_____________\|______________________\|\n_____________36_____________________14\n	276 -- 282	15 -- 21	-13.3674 kcal/mol	3.12995 kcal/mol	3.33058 kcal/mol	266 283@LB@ \| \|@LB@5'-AGG...CCGAC G CCGUC...AAA-3'@LB@ GAC UUCA AAAAGAGG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUG AAGU UUUUCUCC@LB@3'-CGC...CGUCA UCCCAA ACGGC...AAG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -13.3674 kcal/mol@LB@Unfolding Energy - mRNA 3.12995 kcal/mol@LB@Unfolding Energy - sRNA 3.33058 kcal/mol@LB@@LB@Position - mRNA 267 -- 282@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 15 -- 21@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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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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