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
113	0.0192	0.5385	b2573	rpoE	-9.32	0.137991	165 -- 193	49 -- 83	RNA polymerase sigma E factor	_____________164___________________________________194\n_____________\|_____________________________________\|\n5'-ACA...GAUAG________AAA_______UG_________________ACCUC...UGG-3'\n______________CGCG_UGG___UUUGGUU_________GGGAGACUUU\n______________\|:\|\|_\|\|\|___\|\|\|:\|\|\|_________\|:\|\|:\|\|\|:\|\n______________GUGC_ACC___AAAUCAA_________CUCUUUGAGA\n3'-CGC...UUCAA____A___G_________UAAGCUCAA__________GCUUU...AAG-5'\n_____________\|_____________________________________\|\n_____________84____________________________________48\n	184 -- 190	52 -- 58	-21.709 kcal/mol	7.98 kcal/mol	4.40602 kcal/mol	164 194@LB@ \| \|@LB@5'-ACA...GAUAG AAA UG ACCUC...UGG-3'@LB@ CGCG UGG UUUGGUU GGGAGACUUU@LB@ \|:\|\| \|\|\| \|\|\|:\|\|\| \|:\|\|:\|\|\|:\|@LB@ GUGC ACC AAAUCAA CUCUUUGAGA@LB@3'-CGC...UUCAA A G UAAGCUCAA GCUUU...AAG-5'@LB@ \| \|@LB@ 84 48@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -21.709 kcal/mol@LB@Unfolding Energy - mRNA 7.98 kcal/mol@LB@Unfolding Energy - sRNA 4.40602 kcal/mol@LB@@LB@Position - mRNA 165 -- 193@LB@Position - sRNA 49 -- 83@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 52 -- 58@LB@
79	0.01412	0.5385	b2830	rppH	-5.99	0.454649	93 -- 100	64 -- 71	RNA pyrophosphohydrolase	_____________92_______101\n_____________\|________\|\n5'-UUC...CUGUG________AAUUG...GGC-3'\n______________AGUUAUUC\n______________\|\|\|\|\|\|\|\|\n______________UCAAUAAG\n3'-CGC...CGAAA________CUCAA...AAG-5'\n_____________\|________\|\n_____________72_______63\n	94 -- 100	64 -- 70	-7.84269 kcal/mol	1.74359 kcal/mol	0.11296 kcal/mol	92 101@LB@ \| \|@LB@5'-UUC...CUGUG AAUUG...GGC-3'@LB@ AGUUAUUC@LB@ \|\|\|\|\|\|\|\|@LB@ UCAAUAAG@LB@3'-CGC...CGAAA CUCAA...AAG-5'@LB@ \| \|@LB@ 72 63@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -7.84269 kcal/mol@LB@Unfolding Energy - mRNA 1.74359 kcal/mol@LB@Unfolding Energy - sRNA 0.11296 kcal/mol@LB@@LB@Position - mRNA 93 -- 100@LB@Position - sRNA 64 -- 71@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 64 -- 70@LB@
199	0.03481	0.5559	b0407	yajC	-8.41	0.195839	88 -- 104	15 -- 30	SecYEG protein translocase auxillary subunit	_____________87________________105\n_____________\|_________________\|\n5'-UCU...UUACG_____CUAUU_______GUAAA...UUU-3'\n______________CAAGG_____GAAGAGG\n______________\|\|\|\|\|_____:\|\|\|\|\|\|\n______________GUUCC_____UUUCUCC\n3'-CGC...CUGAA_____CAAU________ACGGC...AAG-5'\n_____________\|_________________\|\n_____________31________________14\n	98 -- 104	15 -- 21	-15.1331 kcal/mol	3.4367 kcal/mol	3.28624 kcal/mol	87 105@LB@ \| \|@LB@5'-UCU...UUACG CUAUU GUAAA...UUU-3'@LB@ CAAGG GAAGAGG@LB@ \|\|\|\|\| :\|\|\|\|\|\|@LB@ GUUCC UUUCUCC@LB@3'-CGC...CUGAA CAAU ACGGC...AAG-5'@LB@ \| \|@LB@ 31 14@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -15.1331 kcal/mol@LB@Unfolding Energy - mRNA 3.4367 kcal/mol@LB@Unfolding Energy - sRNA 3.28624 kcal/mol@LB@@LB@Position - mRNA 88 -- 104@LB@Position - sRNA 15 -- 30@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 15 -- 21@LB@
105	0.01788	0.5385	b0619	citA	-6.78	0.351941	4 -- 24	64 -- 89	sensory histidine kinase in two-component regulatory system with CitB	_____________3__________________________25\n_____________\|__________________________\|\n________5'-CAU______AG__________________AUUUA...UCA-3'\n______________AGAGUU_____UGGUUUU__UUAUUU\n______________\|:\|\|\|\|_____\|\|\|:\|\|\|__\|\|\|\|\|:\n______________UUUCAA_____ACCGAAA__AAUAAG\n3'-CGC...GGCGU______GUGCA_______UC______CUCAA...AAG-5'\n_____________\|__________________________\|\n_____________90_________________________63\n	12 -- 18	72 -- 78	-10.9037 kcal/mol	3.54899 kcal/mol	0.576654 kcal/mol	3 25@LB@ \| \|@LB@ 5'-CAU AG AUUUA...UCA-3'@LB@ AGAGUU UGGUUUU UUAUUU@LB@ \|:\|\|\|\| \|\|\|:\|\|\| \|\|\|\|\|:@LB@ UUUCAA ACCGAAA AAUAAG@LB@3'-CGC...GGCGU GUGCA UC CUCAA...AAG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -10.9037 kcal/mol@LB@Unfolding Energy - mRNA 3.54899 kcal/mol@LB@Unfolding Energy - sRNA 0.576654 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 12 -- 18@LB@Position Seed - sRNA 72 -- 78@LB@
168	0.0298	0.5559	b0161	degP	-8.84	0.166335	239 -- 253	75 -- 88	serine endoprotease (protease Do) membrane-associated	_____________238_____________254\n_____________\|_______________\|\n5'-AUU...GCUCU_______G_U_____GUUAU...CGA-3'\n______________GAGUUUA_G_UUGGC\n______________:\|\|\|\|:\|_\|_\|\|\|\|\|\n______________UUCAAGU_C_AACCG\n3'-CGC...GCGUU_______G_______AAAUC...AAG-5'\n_____________\|_______________\|\n_____________89______________74\n	239 -- 245	82 -- 88	-14.9204 kcal/mol	5.56475 kcal/mol	0.515884 kcal/mol	238 254@LB@ \| \|@LB@5'-AUU...GCUCU G U GUUAU...CGA-3'@LB@ GAGUUUA G UUGGC@LB@ :\|\|\|\|:\| \| \|\|\|\|\|@LB@ UUCAAGU C AACCG@LB@3'-CGC...GCGUU G AAAUC...AAG-5'@LB@ \| \|@LB@ 89 74@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -14.9204 kcal/mol@LB@Unfolding Energy - mRNA 5.56475 kcal/mol@LB@Unfolding Energy - sRNA 0.515884 kcal/mol@LB@@LB@Position - mRNA 239 -- 253@LB@Position - sRNA 75 -- 88@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 82 -- 88@LB@
17	0.003067	0.5385	b1628	rsxB	-11.62	0.055094	175 -- 198	58 -- 77	SoxR iron-sulfur cluster reduction factor component; putative iron-sulfur protein	_____________174______________________199\n_____________\|________________________\|\n5'-CAC...UUAUG_________G_____GUGA_____UAAUG...ACG-3'\n______________GGCUUUAGU_GUUUG____AGUUG\n______________\|\|\|\|\|\|\|\|\|_:\|\|:\|____\|\|\|\|\|\n______________CCGAAAUCA_UAAGC____UCAAC\n3'-CGC...UGCAA_________A______________UCUUU...AAG-5'\n_____________\|________________________\|\n_____________78_______________________57\n	177 -- 183	69 -- 75	-20.3316 kcal/mol	7.50919 kcal/mol	1.19974 kcal/mol	174 199@LB@ \| \|@LB@5'-CAC...UUAUG G GUGA UAAUG...ACG-3'@LB@ GGCUUUAGU GUUUG AGUUG@LB@ \|\|\|\|\|\|\|\|\| :\|\|:\| \|\|\|\|\|@LB@ CCGAAAUCA UAAGC UCAAC@LB@3'-CGC...UGCAA A UCUUU...AAG-5'@LB@ \| \|@LB@ 78 57@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -20.3316 kcal/mol@LB@Unfolding Energy - mRNA 7.50919 kcal/mol@LB@Unfolding Energy - sRNA 1.19974 kcal/mol@LB@@LB@Position - mRNA 175 -- 198@LB@Position - sRNA 58 -- 77@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 69 -- 75@LB@
170	0.03041	0.5559	b1629	rsxC	-10.04	0.103937	197 -- 215	64 -- 83	SoxR iron-sulfur cluster reduction factor component; putative membrane-associated NADH oxidoreductase of electron transport complex	_____________196__________________216\n_____________\|____________________\|\n5'-UCA...UGGAA___CAU_____A________UCUGC...CCC-3'\n______________CAC____GCUU_AGUUAUUC\n______________\|\|\|____\|\|\|\|_\|\|\|\|\|\|\|\|\n______________GUG____CGAA_UCAAUAAG\n3'-CGC...UUCAA___CAAC____A________CUCAA...AAG-5'\n_____________\|____________________\|\n_____________84___________________63\n	209 -- 215	64 -- 70	-13.7112 kcal/mol	3.10702 kcal/mol	0.560651 kcal/mol	196 216@LB@ \| \|@LB@5'-UCA...UGGAA CAU A UCUGC...CCC-3'@LB@ CAC GCUU AGUUAUUC@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUG CGAA UCAAUAAG@LB@3'-CGC...UUCAA CAAC A CUCAA...AAG-5'@LB@ \| \|@LB@ 84 63@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -13.7112 kcal/mol@LB@Unfolding Energy - mRNA 3.10702 kcal/mol@LB@Unfolding Energy - sRNA 0.560651 kcal/mol@LB@@LB@Position - mRNA 197 -- 215@LB@Position - sRNA 64 -- 83@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 64 -- 70@LB@
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@
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@
12	0.002293	0.5385	b1823	cspC	-13.69	0.023618	13 -- 32	14 -- 35	stress protein member of the CspA-family	_____________12_____________________33\n_____________\|______________________\|\n5'-UAU...UAACA________________C_____ACAGU...UCU-3'\n______________GAUUUC__GGGUUAAA_GAGGU\n______________\|\|:\|\|\|__\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUGAAG__CCCAAUUU_CUCCA\n3'-CGC...CGUCA______UU________U_____CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	20 -- 26	20 -- 26	-23.8593 kcal/mol	6.83349 kcal/mol	3.33183 kcal/mol	12 33@LB@ \| \|@LB@5'-UAU...UAACA C ACAGU...UCU-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 -13.69 kcal/mol@LB@Hybridization Energy -23.8593 kcal/mol@LB@Unfolding Energy - mRNA 6.83349 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 13 -- 32@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 20 -- 26@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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