Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
14	0.003078	0.593	b0886	cydC	-10.90	0.026971	183 -- 199	39 -- 56	glutathione/cysteine ABC transporter export permease/ATPase	_____________182________________200\n_____________\|__________________\|\n5'-GCG...CCCAU_____________A____AAUGC...UCG-3'\n______________CGUC_AGGAGGAG_UUUA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|:\|\n______________GCAG_UUCUCCUU_AAGU\n3'-UUU...ACCGG____U________A____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	188 -- 194	44 -- 50	-16.2318 kcal/mol	4.17801 kcal/mol	1.15786 kcal/mol	182 200@LB@ \| \|@LB@5'-GCG...CCCAU A AAUGC...UCG-3'@LB@ CGUC AGGAGGAG UUUA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|:\|@LB@ GCAG UUCUCCUU AAGU@LB@3'-UUU...ACCGG U A AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -16.2318 kcal/mol@LB@Unfolding Energy - mRNA 4.17801 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 183 -- 199@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
53	0.01077	0.6177	b3429	glgA	-6.74	0.182373	105 -- 111	44 -- 50	glycogen synthase	_____________104_____112\n_____________\|_______\|\n5'-GUA...AACGC_______GAUGC...ACG-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	105 -- 111	44 -- 50	-9.00959 kcal/mol	1.43957 kcal/mol	0.825028 kcal/mol	104 112@LB@ \| \|@LB@5'-GUA...AACGC GAUGC...ACG-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -6.74 kcal/mol@LB@Hybridization Energy -9.00959 kcal/mol@LB@Unfolding Energy - mRNA 1.43957 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 44 -- 50@LB@
70	0.01448	0.6177	b4012	yjaB	-8.12	0.098308	234 -- 242	44 -- 52	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein	_____________233_______243\n_____________\|_________\|\n5'-AAG...AUGAG_________GAACU...CAG-3'\n______________GAAGGGGAG\n______________:\|\|\|:\|\|\|:\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	236 -- 242	44 -- 50	-9.78668 kcal/mol	0.80114 kcal/mol	0.860683 kcal/mol	233 243@LB@ \| \|@LB@5'-AAG...AUGAG GAACU...CAG-3'@LB@ GAAGGGGAG@LB@ :\|\|\|:\|\|\|:@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.78668 kcal/mol@LB@Unfolding Energy - mRNA 0.80114 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 234 -- 242@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 44 -- 50@LB@
20	0.00399	0.5992	b4175	hflC	-10.54	0.031960	184 -- 196	43 -- 56	HflB protease modulator specific for phage lambda cII repressor	_____________183____________197\n_____________\|______________\|\n5'-UUA...ACCAG______________AACGA...GUU-3'\n______________CGUCAGGG_GGAAU\n______________\|\|\|\|\|::\|_\|\|\|\|\|\n______________GCAGUUUC_CCUUA\n3'-UUU...ACCGG________U_____AAGUA...ACA-5'\n_____________\|______________\|\n_____________57_____________42\n	185 -- 191	49 -- 55	-15.8123 kcal/mol	4.32193 kcal/mol	0.953958 kcal/mol	183 197@LB@ \| \|@LB@5'-UUA...ACCAG AACGA...GUU-3'@LB@ CGUCAGGG GGAAU@LB@ \|\|\|\|\|::\| \|\|\|\|\|@LB@ GCAGUUUC CCUUA@LB@3'-UUU...ACCGG U AAGUA...ACA-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -10.54 kcal/mol@LB@Hybridization Energy -15.8123 kcal/mol@LB@Unfolding Energy - mRNA 4.32193 kcal/mol@LB@Unfolding Energy - sRNA 0.953958 kcal/mol@LB@@LB@Position - mRNA 184 -- 196@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 49 -- 55@LB@
66	0.01414	0.6177	b0440	hupB	-10.30	0.035643	184 -- 193	44 -- 53	HU DNA-binding transcriptional regulator beta subunit	_____________183________194\n_____________\|__________\|\n5'-CGC...AAUUA__________GAGAA...CUG-3'\n______________UAAAGAGGAA\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	187 -- 193	44 -- 50	-11.552 kcal/mol	0.319105 kcal/mol	0.927997 kcal/mol	183 194@LB@ \| \|@LB@5'-CGC...AAUUA GAGAA...CUG-3'@LB@ UAAAGAGGAA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -11.552 kcal/mol@LB@Unfolding Energy - mRNA 0.319105 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 184 -- 193@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 44 -- 50@LB@
104	0.02144	0.6177	b2718	hycH	-8.07	0.100760	181 -- 190	46 -- 55	hydrogenase 3 maturation protein	_____________180________191\n_____________\|__________\|\n5'-CAG...AUGUU__________CGCGU...UGG-3'\n______________GUUGAAGAGG\n______________\|\|::\|\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	184 -- 190	46 -- 52	-11.8031 kcal/mol	2.8078 kcal/mol	0.924411 kcal/mol	180 191@LB@ \| \|@LB@5'-CAG...AUGUU CGCGU...UGG-3'@LB@ GUUGAAGAGG@LB@ \|\|::\|\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -11.8031 kcal/mol@LB@Unfolding Energy - mRNA 2.8078 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 181 -- 190@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 46 -- 52@LB@
35	0.00713	0.6129	b2025	hisF	-8.66	0.076851	182 -- 193	46 -- 57	imidazole glycerol phosphate synthase catalytic subunit with HisH	_____________181__________194\n_____________\|____________\|\n5'-UCG...AUUCA____G_______CCAUC...UGC-3'\n______________CCGU_AAGGAGG\n______________\|\|\|\|_\|\|:\|\|\|\|\n______________GGCA_UUUCUCC\n3'-UUU...AACCG____G_______UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	187 -- 193	46 -- 52	-16.1254 kcal/mol	4.72855 kcal/mol	2.7365 kcal/mol	181 194@LB@ \| \|@LB@5'-UCG...AUUCA G CCAUC...UGC-3'@LB@ CCGU AAGGAGG@LB@ \|\|\|\| \|\|:\|\|\|\|@LB@ GGCA UUUCUCC@LB@3'-UUU...AACCG G UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -16.1254 kcal/mol@LB@Unfolding Energy - mRNA 4.72855 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 46 -- 52@LB@
49	0.009604	0.6129	b1175	minD	-8.49	0.083180	191 -- 199	40 -- 48	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAACA_________UAUGG...AAA-3'\n______________AGGAAUUUC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCUUAAAG\n3'-UUU...GUUUC_________UAAAA...ACA-5'\n_____________\|_________\|\n_____________49________39\n	193 -- 199	40 -- 46	-11.0161 kcal/mol	1.62901 kcal/mol	0.898161 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAACA UAUGG...AAA-3'@LB@ AGGAAUUUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCUUAAAG@LB@3'-UUU...GUUUC UAAAA...ACA-5'@LB@ \| \|@LB@ 49 39@LB@@LB@@LB@Energy -8.49 kcal/mol@LB@Hybridization Energy -11.0161 kcal/mol@LB@Unfolding Energy - mRNA 1.62901 kcal/mol@LB@Unfolding Energy - sRNA 0.898161 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 40 -- 48@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 40 -- 46@LB@
131	0.02569	0.6177	b0848	ybjM	-8.44	0.085177	187 -- 197	44 -- 55	inner membrane protein	_____________186__________198\n_____________\|____________\|\n5'-GAA...GCAGU____________CGAGU...GGG-3'\n______________GUC_AGGAGGAA\n______________\|\|\|_\|:\|\|\|\|\|\|\n______________CAG_UUCUCCUU\n3'-UUU...CCGGG___U________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	191 -- 197	44 -- 50	-13.6185 kcal/mol	4.23971 kcal/mol	0.941432 kcal/mol	186 198@LB@ \| \|@LB@5'-GAA...GCAGU CGAGU...GGG-3'@LB@ GUC AGGAGGAA@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ CAG UUCUCCUU@LB@3'-UUU...CCGGG U AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -13.6185 kcal/mol@LB@Unfolding Energy - mRNA 4.23971 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 187 -- 197@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
117	0.02321	0.6177	b1712	ihfA	-8.91	0.068436	115 -- 126	45 -- 56	integration host factor (IHF) DNA-binding protein alpha subunit	_____________114__________127\n_____________\|____________\|\n5'-CGU...ACACU__AA________GAUUG...AGA-3'\n______________CG__GAAGAGGA\n______________\|\|__:\|\|\|\|\|\|\|\n______________GC__UUUCUCCU\n3'-UUU...ACCGG__AG________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	120 -- 126	45 -- 51	-12.2887 kcal/mol	2.43966 kcal/mol	0.938337 kcal/mol	114 127@LB@ \| \|@LB@5'-CGU...ACACU AA GAUUG...AGA-3'@LB@ CG GAAGAGGA@LB@ \|\| :\|\|\|\|\|\|\|@LB@ GC UUUCUCCU@LB@3'-UUU...ACCGG AG UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -12.2887 kcal/mol@LB@Unfolding Energy - mRNA 2.43966 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 115 -- 126@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 45 -- 51@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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