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
151	0.02561	0.5485	b4041	plsB	-9.39	0.134646	197 -- 210	74 -- 86	glycerol-3-phosphate O-acyltransferase	_____________196____________211\n_____________\|______________\|\n5'-UCG...ACAUC________CC____GGCCA...UGG-3'\n______________GUUUAUGU__GGCU\n______________\|\|\|:\|:\|\|__\|\|\|\|\n______________CAAGUGCA__CCGA\n3'-CGC...GUUUU________A_____AAUCA...AAG-5'\n_____________\|______________\|\n_____________87_____________73\n	198 -- 204	79 -- 85	-13.0466 kcal/mol	3.14742 kcal/mol	0.513318 kcal/mol	196 211@LB@ \| \|@LB@5'-UCG...ACAUC CC GGCCA...UGG-3'@LB@ GUUUAUGU GGCU@LB@ \|\|\|:\|:\|\| \|\|\|\|@LB@ CAAGUGCA CCGA@LB@3'-CGC...GUUUU A AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -13.0466 kcal/mol@LB@Unfolding Energy - mRNA 3.14742 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 79 -- 85@LB@
169	0.03038	0.5559	b2912	fau	-9.38	0.135051	85 -- 98	22 -- 35	5-formyltetrahydrofolate cyclo-ligase family protein	_____________84_____________99\n_____________\|______________\|\n5'-GAA...ACCAA__G___________CAGCC...UGG-3'\n______________GG_UUCAAGGGUUA\n______________\|:_\|\|\|\|\|\|\|\|\|\|\|\n______________CU_AAGUUCCCAAU\n3'-CGC...CGUCA__G___________UUUCU...AAG-5'\n_____________\|______________\|\n_____________36_____________21\n	92 -- 98	22 -- 28	-18.6025 kcal/mol	5.89438 kcal/mol	3.32987 kcal/mol	84 99@LB@ \| \|@LB@5'-GAA...ACCAA G CAGCC...UGG-3'@LB@ GG UUCAAGGGUUA@LB@ \|: \|\|\|\|\|\|\|\|\|\|\|@LB@ CU AAGUUCCCAAU@LB@3'-CGC...CGUCA G UUUCU...AAG-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -18.6025 kcal/mol@LB@Unfolding Energy - mRNA 5.89438 kcal/mol@LB@Unfolding Energy - sRNA 3.32987 kcal/mol@LB@@LB@Position - mRNA 85 -- 98@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 22 -- 28@LB@
183	0.03203	0.5559	b4484	cpxP	-9.38	0.135070	107 -- 120	71 -- 85	inhibitor of the cpx response; periplasmic adaptor protein	_____________106_____________121\n_____________\|_______________\|\n5'-UAA...AUGAC_______________CACCC...GUG-3'\n______________UUUACGUUG_UUUUA\n______________\|\|:\|\|\|\|\|\|_:\|\|\|\|\n______________AAGUGCAAC_GAAAU\n3'-CGC...UUUUC_________C_____CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	109 -- 115	77 -- 83	-11.4265 kcal/mol	1.48788 kcal/mol	0.560731 kcal/mol	106 121@LB@ \| \|@LB@5'-UAA...AUGAC CACCC...GUG-3'@LB@ UUUACGUUG UUUUA@LB@ \|\|:\|\|\|\|\|\| :\|\|\|\|@LB@ AAGUGCAAC GAAAU@LB@3'-CGC...UUUUC C CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -11.4265 kcal/mol@LB@Unfolding Energy - mRNA 1.48788 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 107 -- 120@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 77 -- 83@LB@
175	0.03099	0.5559	b2149	mglA	-9.34	0.136967	92 -- 105	70 -- 84	methyl-galactoside ABC transporter ATPase	_____________91______________106\n_____________\|_______________\|\n5'-CGA...GUACC__________G____AUAAA...AUU-3'\n______________UUAUGUUGGC__UAG\n______________\|:\|:\|\|\|\|\|\|__\|\|\|\n______________AGUGCAACCG__AUC\n3'-CGC...UUUCA__________AA___AAUAA...AAG-5'\n_____________\|_______________\|\n_____________85______________69\n	95 -- 101	75 -- 81	-15.5186 kcal/mol	5.61316 kcal/mol	0.563314 kcal/mol	91 106@LB@ \| \|@LB@5'-CGA...GUACC G AUAAA...AUU-3'@LB@ UUAUGUUGGC UAG@LB@ \|:\|:\|\|\|\|\|\| \|\|\|@LB@ AGUGCAACCG AUC@LB@3'-CGC...UUUCA AA AAUAA...AAG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -15.5186 kcal/mol@LB@Unfolding Energy - mRNA 5.61316 kcal/mol@LB@Unfolding Energy - sRNA 0.563314 kcal/mol@LB@@LB@Position - mRNA 92 -- 105@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 75 -- 81@LB@
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@
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@
112	0.0191	0.5385	b0854	potF	-9.27	0.140763	36 -- 50	64 -- 78	putrescine ABC transporter periplasmic binding protein	_____________35______________51\n_____________\|_______________\|\n5'-UAC...AACCC_____AA________UUGCG...ACA-3'\n______________UGGCU__AGUUAUUC\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\|\n______________ACCGA__UCAAUAAG\n3'-CGC...GUGCA_____AA________CUCAA...AAG-5'\n_____________\|_______________\|\n_____________79______________63\n	44 -- 50	64 -- 70	-15.0609 kcal/mol	5.5152 kcal/mol	0.273858 kcal/mol	35 51@LB@ \| \|@LB@5'-UAC...AACCC AA UUGCG...ACA-3'@LB@ UGGCU AGUUAUUC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ ACCGA UCAAUAAG@LB@3'-CGC...GUGCA AA CUCAA...AAG-5'@LB@ \| \|@LB@ 79 63@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.0609 kcal/mol@LB@Unfolding Energy - mRNA 5.5152 kcal/mol@LB@Unfolding Energy - sRNA 0.273858 kcal/mol@LB@@LB@Position - mRNA 36 -- 50@LB@Position - sRNA 64 -- 78@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 64 -- 70@LB@
9	0.0016	0.5385	b1709	btuD	-9.25	0.141890	185 -- 194	75 -- 84	vitamin B12 ABC transporter ATPase	_____________184________195\n_____________\|__________\|\n5'-GCA...UAAAC_G________AAAAU...GGC-3'\n______________U_GCGUUGGC\n______________\|_:\|\|\|\|\|\|\|\n______________A_UGCAACCG\n3'-CGC...UUUCA_G________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	188 -- 194	75 -- 81	-15.1998 kcal/mol	5.44246 kcal/mol	0.505918 kcal/mol	184 195@LB@ \| \|@LB@5'-GCA...UAAAC G AAAAU...GGC-3'@LB@ U GCGUUGGC@LB@ \| :\|\|\|\|\|\|\|@LB@ A UGCAACCG@LB@3'-CGC...UUUCA G AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -15.1998 kcal/mol@LB@Unfolding Energy - mRNA 5.44246 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 75 -- 84@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@
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@

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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usability assessment

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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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