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
142	0.02338	0.5385	b1126	potA	-10.56	0.084569	277 -- 295	14 -- 34	spermidine/putrescine ABC transporter ATPase	_____________276___________________296\n_____________\|_____________________\|\n5'-CAA...CAAAU_______U_____________CAUUC-3'\n______________GCUUUGA_GGU__AAAGAGGU\n______________:\|\|\|::\|_\|\|\|__\|\|\|\|\|\|\|\|\n______________UGAAGUU_CCA__UUUCUCCA\n3'-CGC...GUCAC_______C___AU________CGGCG...AAG-5'\n_____________\|_____________________\|\n_____________35____________________13\n	289 -- 295	14 -- 20	-18.1028 kcal/mol	4.21038 kcal/mol	3.33169 kcal/mol	276 296@LB@ \| \|@LB@5'-CAA...CAAAU U CAUUC-3'@LB@ GCUUUGA GGU AAAGAGGU@LB@ :\|\|\|::\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UGAAGUU CCA UUUCUCCA@LB@3'-CGC...GUCAC C AU CGGCG...AAG-5'@LB@ \| \|@LB@ 35 13@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -18.1028 kcal/mol@LB@Unfolding Energy - mRNA 4.21038 kcal/mol@LB@Unfolding Energy - sRNA 3.33169 kcal/mol@LB@@LB@Position - mRNA 277 -- 295@LB@Position - sRNA 14 -- 34@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 14 -- 20@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@
46	0.009803	0.5385	b1418	cybB	-9.32	0.138160	281 -- 295	73 -- 89	cytochrome b561	_____________280_______________296\n_____________\|_________________\|\n5'-AAC...GCAAU_________________CUUCC-3'\n______________GGAGUUU_CG_UGGUUU\n______________::\|\|\|\|:_\|\|_\|\|\|:\|\|\n______________UUUCAAG_GC_ACCGAA\n3'-CGC...GGCGU_______U__A______AUCAA...AAG-5'\n_____________\|_________________\|\n_____________90________________72\n	281 -- 287	83 -- 89	-12.2046 kcal/mol	2.36714 kcal/mol	0.517627 kcal/mol	280 296@LB@ \| \|@LB@5'-AAC...GCAAU CUUCC-3'@LB@ GGAGUUU CG UGGUUU@LB@ ::\|\|\|\|: \|\| \|\|\|:\|\|@LB@ UUUCAAG GC ACCGAA@LB@3'-CGC...GGCGU U A AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -12.2046 kcal/mol@LB@Unfolding Energy - mRNA 2.36714 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 281 -- 295@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 83 -- 89@LB@
189	0.03342	0.5559	b2172	yeiQ	-17.65	0.004645	282 -- 298	70 -- 86	putative NAD-dependent D-mannonate oxidoreductase	_____________281_______________299\n_____________\|_________________\|\n5'-GAU...GUAUC______U__________AG-3'\n______________GUUCAU_UUGGCUUUGG\n______________\|\|\|\|\|:_\|\|\|\|\|\|\|\|:\|\n______________CAAGUG_AACCGAAAUC\n3'-CGC...GUUUU______C__________AAUAA...AAG-5'\n_____________\|_________________\|\n_____________87________________69\n	292 -- 298	70 -- 76	-21.6632 kcal/mol	3.44897 kcal/mol	0.568254 kcal/mol	281 299@LB@ \| \|@LB@5'-GAU...GUAUC U AG-3'@LB@ GUUCAU UUGGCUUUGG@LB@ \|\|\|\|\|: \|\|\|\|\|\|\|\|:\|@LB@ CAAGUG AACCGAAAUC@LB@3'-CGC...GUUUU C AAUAA...AAG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -17.65 kcal/mol@LB@Hybridization Energy -21.6632 kcal/mol@LB@Unfolding Energy - mRNA 3.44897 kcal/mol@LB@Unfolding Energy - sRNA 0.568254 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 70 -- 76@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@
100	0.01671	0.5385	b3211	yhcC	-9.80	0.114390	283 -- 295	70 -- 82	putative Fe-S oxidoreductase Radical SAM superfamily protein	_____________282___________296\n_____________\|_____________\|\n5'-UGC...GCUGC___GC________CUGCC-3'\n______________ACG__GGUUUUAG\n______________\|\|\|__\|\|:\|\|\|\|\|\n______________UGC__CCGAAAUC\n3'-CGC...UCAAG___AA________AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	289 -- 295	70 -- 76	-11.7424 kcal/mol	1.55142 kcal/mol	0.389672 kcal/mol	282 296@LB@ \| \|@LB@5'-UGC...GCUGC GC CUGCC-3'@LB@ ACG GGUUUUAG@LB@ \|\|\| \|\|:\|\|\|\|\|@LB@ UGC CCGAAAUC@LB@3'-CGC...UCAAG AA AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -9.80 kcal/mol@LB@Hybridization Energy -11.7424 kcal/mol@LB@Unfolding Energy - mRNA 1.55142 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 70 -- 76@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@
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@
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@
173	0.03066	0.5559	b2928	yggC	-11.87	0.049837	290 -- 298	75 -- 83	putative PanK family P-loop kinase	_____________289_______299\n_____________\|_________\|\n5'-GAA...CUGCA_________GG-3'\n______________CAUGUUGGC\n______________\|\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	292 -- 298	75 -- 81	-14.124 kcal/mol	1.76242 kcal/mol	0.492259 kcal/mol	289 299@LB@ \| \|@LB@5'-GAA...CUGCA GG-3'@LB@ CAUGUUGGC@LB@ \|\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -14.124 kcal/mol@LB@Unfolding Energy - mRNA 1.76242 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 290 -- 298@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 75 -- 81@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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