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
91	0.0156	0.5385	b0881	clpS	-13.09	0.030255	248 -- 265	74 -- 90	regulatory protein for ClpA substrate specificity	_____________247________________266\n_____________\|__________________\|\n5'-GCA...GAAGA___________AC_C___AAAAC...UCA-3'\n______________AAAAGUUCGCG__G_GCU\n______________\|\|\|\|\|\|\|\|:\|\|__\|_\|\|\|\n______________UUUUCAAGUGC__C_CGA\n3'-CGC...AGGCG___________AA_____AAUCA...AAG-5'\n_____________\|__________________\|\n_____________91_________________73\n	252 -- 258	80 -- 86	-16.9257 kcal/mol	3.31752 kcal/mol	0.517587 kcal/mol	247 266@LB@ \| \|@LB@5'-GCA...GAAGA AC C AAAAC...UCA-3'@LB@ AAAAGUUCGCG G GCU@LB@ \|\|\|\|\|\|\|\|:\|\| \| \|\|\|@LB@ UUUUCAAGUGC C CGA@LB@3'-CGC...AGGCG AA AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -13.09 kcal/mol@LB@Hybridization Energy -16.9257 kcal/mol@LB@Unfolding Energy - mRNA 3.31752 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 248 -- 265@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 80 -- 86@LB@
92	0.01569	0.5385	b1246	oppD	-11.32	0.062179	266 -- 290	69 -- 90	oligopeptide ABC transporter ATPase	_____________265_______________________291\n_____________\|_________________________\|\n5'-AGC...AACGU_____A_______GUCAC_______ACCCC...ACG-3'\n______________GAAAG_UUUGCGU_____CUUUAGU\n______________:\|\|\|\|_\|\|::\|\|\|_____\|\|\|\|\|\|\|\n______________UUUUC_AAGUGCA_____GAAAUCA\n3'-CGC...AGGCG_____________ACC_________AUAAG...AAG-5'\n_____________\|_________________________\|\n_____________91________________________68\n	284 -- 290	69 -- 75	-14.6652 kcal/mol	2.76867 kcal/mol	0.572281 kcal/mol	265 291@LB@ \| \|@LB@5'-AGC...AACGU A GUCAC ACCCC...ACG-3'@LB@ GAAAG UUUGCGU CUUUAGU@LB@ :\|\|\|\| \|\|::\|\|\| \|\|\|\|\|\|\|@LB@ UUUUC AAGUGCA GAAAUCA@LB@3'-CGC...AGGCG ACC AUAAG...AAG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -14.6652 kcal/mol@LB@Unfolding Energy - mRNA 2.76867 kcal/mol@LB@Unfolding Energy - sRNA 0.572281 kcal/mol@LB@@LB@Position - mRNA 266 -- 290@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@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@
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@
95	0.01635	0.5385	b2287	nuoB	-8.27	0.206762	33 -- 42	71 -- 80	NADH:ubiquinone oxidoreductase chain B	_____________32_________43\n_____________\|__________\|\n5'-CAU...GCUGG__A_______UGGAA...UUA-3'\n______________GU_GGCUUUG\n______________\|\|_\|\|\|\|\|\|:\n______________CA_CCGAAAU\n3'-CGC...AAGUG__A_______CAAUA...AAG-5'\n_____________\|__________\|\n_____________81_________70\n	36 -- 42	71 -- 77	-10.0496 kcal/mol	1.54713 kcal/mol	0.236872 kcal/mol	32 43@LB@ \| \|@LB@5'-CAU...GCUGG A UGGAA...UUA-3'@LB@ GU GGCUUUG@LB@ \|\| \|\|\|\|\|\|:@LB@ CA CCGAAAU@LB@3'-CGC...AAGUG A CAAUA...AAG-5'@LB@ \| \|@LB@ 81 70@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -10.0496 kcal/mol@LB@Unfolding Energy - mRNA 1.54713 kcal/mol@LB@Unfolding Energy - sRNA 0.236872 kcal/mol@LB@@LB@Position - mRNA 33 -- 42@LB@Position - sRNA 71 -- 80@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 71 -- 77@LB@
96	0.0164	0.5385	b2670	alaE	-9.59	0.124335	245 -- 257	74 -- 86	alanine exporter alanine-inducible stress-responsive	_____________244___________258\n_____________\|_____________\|\n5'-CGG...GAUAC_______A_____GUUUA...UCU-3'\n______________GUUCGCG_UGGUU\n______________\|\|\|\|:\|\|_\|\|\|:\|\n______________CAAGUGC_ACCGA\n3'-CGC...GUUUU_______A_____AAUCA...AAG-5'\n_____________\|_____________\|\n_____________87____________73\n	245 -- 251	80 -- 86	-15.4589 kcal/mol	5.35611 kcal/mol	0.513318 kcal/mol	244 258@LB@ \| \|@LB@5'-CGG...GAUAC A GUUUA...UCU-3'@LB@ GUUCGCG UGGUU@LB@ \|\|\|\|:\|\| \|\|\|:\|@LB@ CAAGUGC ACCGA@LB@3'-CGC...GUUUU A AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -15.4589 kcal/mol@LB@Unfolding Energy - mRNA 5.35611 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 245 -- 257@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 80 -- 86@LB@
97	0.01643	0.5385	b2704	srlB	-9.20	0.144516	91 -- 103	75 -- 87	glucitol/sorbitol-specific enzyme IIA component of PTS	_____________90____________104\n_____________\|_____________\|\n5'-GGC...GACAC_________C___GUCCC...CUG-3'\n______________GGUUCGCGU_GGU\n______________:\|\|\|\|:\|\|\|_\|\|:\n______________UCAAGUGCA_CCG\n3'-CGC...CGUUU_________A___AAAUC...AAG-5'\n_____________\|_____________\|\n_____________88____________74\n	93 -- 99	79 -- 85	-16.5171 kcal/mol	6.8003 kcal/mol	0.512669 kcal/mol	90 104@LB@ \| \|@LB@5'-GGC...GACAC C GUCCC...CUG-3'@LB@ GGUUCGCGU GGU@LB@ :\|\|\|\|:\|\|\| \|\|:@LB@ UCAAGUGCA CCG@LB@3'-CGC...CGUUU A AAAUC...AAG-5'@LB@ \| \|@LB@ 88 74@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -16.5171 kcal/mol@LB@Unfolding Energy - mRNA 6.8003 kcal/mol@LB@Unfolding Energy - sRNA 0.512669 kcal/mol@LB@@LB@Position - mRNA 91 -- 103@LB@Position - sRNA 75 -- 87@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 79 -- 85@LB@
98	0.0165	0.5385	b0151	fhuC	-12.15	0.044517	184 -- 202	66 -- 85	iron(3+)-hydroxamate import ABC transporter ATPase	_____________183____________________203\n_____________\|______________________\|\n5'-CUG...CCCAU_____AA_______________GCAGG...CCU-3'\n______________UUCAC__GUUGGCU___GUUAU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|___\|\|\|\|\|\n______________AAGUG__CAACCGA___CAAUA\n3'-CGC...UUUUC______________AAU_____AGCUC...AAG-5'\n_____________\|______________________\|\n_____________86_____________________65\n	191 -- 197	74 -- 80	-16.912 kcal/mol	4.1925 kcal/mol	0.573112 kcal/mol	183 203@LB@ \| \|@LB@5'-CUG...CCCAU AA GCAGG...CCU-3'@LB@ UUCAC GUUGGCU GUUAU@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AAGUG CAACCGA CAAUA@LB@3'-CGC...UUUUC AAU AGCUC...AAG-5'@LB@ \| \|@LB@ 86 65@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -16.912 kcal/mol@LB@Unfolding Energy - mRNA 4.1925 kcal/mol@LB@Unfolding Energy - sRNA 0.573112 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 66 -- 85@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 74 -- 80@LB@
99	0.01653	0.5385	b0004	thrC	-7.16	0.308279	183 -- 210	49 -- 64	L-threonine synthase	_____________182__________________________211\n_____________\|____________________________\|\n5'-CGC...GCGCA_____AC___AAAACUAAAU________ACAAU...ACG-3'\n______________CGAGU__UGG__________GAAACUCU\n______________\|\|\|\|\|__\|\|:__________\|\|\|\|\|\|\|\|\n______________GCUCA__ACU__________CUUUGAGA\n3'-CGC...AAUAA____________________________GCUUU...AAG-5'\n_____________\|____________________________\|\n_____________65___________________________48\n	204 -- 210	49 -- 55	-14.0058 kcal/mol	2.63666 kcal/mol	4.20534 kcal/mol	182 211@LB@ \| \|@LB@5'-CGC...GCGCA AC AAAACUAAAU ACAAU...ACG-3'@LB@ CGAGU UGG GAAACUCU@LB@ \|\|\|\|\| \|\|: \|\|\|\|\|\|\|\|@LB@ GCUCA ACU CUUUGAGA@LB@3'-CGC...AAUAA GCUUU...AAG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -14.0058 kcal/mol@LB@Unfolding Energy - mRNA 2.63666 kcal/mol@LB@Unfolding Energy - sRNA 4.20534 kcal/mol@LB@@LB@Position - mRNA 183 -- 210@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 49 -- 55@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@

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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