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
1	0	0	b0481	ybaK	-91.37	0.000000	1 -- 79	1 -- 79	Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase	______________1______________________________________________________________________________80\n______________\|______________________________________________________________________________\|\n___________5'-_______________________________________________________________________________AACUC...UCG-3'\n______________AAUGGCCAAUAUCGCUAUUGGCCCGUCAAAGAGGAAUUUCAUUUUUUUAUUAUUAUGCCGUCACUUUAAGCGACGGUGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUACCGGUUAUAGCGAUAACCGGGCAGUUUCUCCUUAAAGUAAAAAAAUAAUAAUACGGCAGUGAAAUUCGCUGCCACA\n______3'-UUUUU_______________________________________________________________________________-5'\n_____________\|______________________________________________________________________________\|\n_____________80_____________________________________________________________________________1\n	51 -- 57	23 -- 29	-143.199 kcal/mol	26.5504 kcal/mol	25.2758 kcal/mol	1 80@LB@ \| \|@LB@ 5'- AACUC...UCG-3'@LB@ AAUGGCCAAUAUCGCUAUUGGCCCGUCAAAGAGGAAUUUCAUUUUUUUAUUAUUAUGCCGUCACUUUAAGCGACGGUGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUACCGGUUAUAGCGAUAACCGGGCAGUUUCUCCUUAAAGUAAAAAAAUAAUAAUACGGCAGUGAAAUUCGCUGCCACA@LB@ 3'-UUUUU -5'@LB@ \| \|@LB@ 80 1@LB@@LB@@LB@Energy -91.37 kcal/mol@LB@Hybridization Energy -143.199 kcal/mol@LB@Unfolding Energy - mRNA 26.5504 kcal/mol@LB@Unfolding Energy - sRNA 25.2758 kcal/mol@LB@@LB@Position - mRNA 1 -- 79@LB@Position - sRNA 1 -- 79@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 23 -- 29@LB@
24	0.004602	0.5992	b0526	cysS	-10.20	0.037463	234 -- 245	41 -- 52	cysteinyl-tRNA synthetase	_____________233__________246\n_____________\|____________\|\n5'-GCC...GCCAA____________AAGCC...ACG-3'\n______________AAAGAGGAAUUU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUUAAA\n3'-UUU...GGCAG____________GUAAA...ACA-5'\n_____________\|____________\|\n_____________53___________40\n	239 -- 245	41 -- 47	-14.6017 kcal/mol	3.53507 kcal/mol	0.867487 kcal/mol	233 246@LB@ \| \|@LB@5'-GCC...GCCAA AAGCC...ACG-3'@LB@ AAAGAGGAAUUU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUUAAA@LB@3'-UUU...GGCAG GUAAA...ACA-5'@LB@ \| \|@LB@ 53 40@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -14.6017 kcal/mol@LB@Unfolding Energy - mRNA 3.53507 kcal/mol@LB@Unfolding Energy - sRNA 0.867487 kcal/mol@LB@@LB@Position - mRNA 234 -- 245@LB@Position - sRNA 41 -- 52@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 41 -- 47@LB@
69	0.01434	0.6177	b0551	quuD	-6.03	0.248082	117 -- 124	48 -- 55	DLP12 prophage; putative antitermination protein	_____________116______125\n_____________\|________\|\n5'-ACU...AUGAA________UAACA...GAU-3'\n______________GUCAGAGA\n______________\|\|\|\|:\|\|\|\n______________CAGUUUCU\n3'-UUU...CCGGG________CCUUA...ACA-5'\n_____________\|________\|\n_____________56_______47\n	118 -- 124	48 -- 54	-9.27195 kcal/mol	2.92769 kcal/mol	0.318869 kcal/mol	116 125@LB@ \| \|@LB@5'-ACU...AUGAA UAACA...GAU-3'@LB@ GUCAGAGA@LB@ \|\|\|\|:\|\|\|@LB@ CAGUUUCU@LB@3'-UUU...CCGGG CCUUA...ACA-5'@LB@ \| \|@LB@ 56 47@LB@@LB@@LB@Energy -6.03 kcal/mol@LB@Hybridization Energy -9.27195 kcal/mol@LB@Unfolding Energy - mRNA 2.92769 kcal/mol@LB@Unfolding Energy - sRNA 0.318869 kcal/mol@LB@@LB@Position - mRNA 117 -- 124@LB@Position - sRNA 48 -- 55@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 48 -- 54@LB@
73	0.01516	0.6177	b0619	citA	-15.44	0.003129	164 -- 175	46 -- 57	sensory histidine kinase in two-component regulatory system with CitB	_____________163__________176\n_____________\|____________\|\n5'-CAU...UACAU____________CUCGG...UCA-3'\n______________CCGUCAAAGAGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GGCAGUUUCUCC\n3'-UUU...AACCG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	169 -- 175	46 -- 52	-20.3901 kcal/mol	2.21322 kcal/mol	2.7365 kcal/mol	163 176@LB@ \| \|@LB@5'-CAU...UACAU CUCGG...UCA-3'@LB@ CCGUCAAAGAGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GGCAGUUUCUCC@LB@3'-UUU...AACCG UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -20.3901 kcal/mol@LB@Unfolding Energy - mRNA 2.21322 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 164 -- 175@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 46 -- 52@LB@
185	0.03847	0.6177	b0621	dcuC	-6.69	0.186516	155 -- 171	26 -- 48	anaerobic C4-dicarboxylate transport	_____________154_____________________172\n_____________\|_______________________\|\n5'-UGC...GCUUU_______________________UACUU...UCG-3'\n______________AGGAAUUUU______UUAUUAUU\n______________\|\|\|\|\|\|\|\|:______\|\|\|\|\|\|\|\|\n______________UCCUUAAAG______AAUAAUAA\n3'-UUU...GUUUC_________UAAAAA________UACGG...ACA-5'\n_____________\|_______________________\|\n_____________49______________________25\n	165 -- 171	26 -- 32	-10.8714 kcal/mol	3.1068 kcal/mol	1.07117 kcal/mol	154 172@LB@ \| \|@LB@5'-UGC...GCUUU UACUU...UCG-3'@LB@ AGGAAUUUU UUAUUAUU@LB@ \|\|\|\|\|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UCCUUAAAG AAUAAUAA@LB@3'-UUU...GUUUC UAAAAA UACGG...ACA-5'@LB@ \| \|@LB@ 49 25@LB@@LB@@LB@Energy -6.69 kcal/mol@LB@Hybridization Energy -10.8714 kcal/mol@LB@Unfolding Energy - mRNA 3.1068 kcal/mol@LB@Unfolding Energy - sRNA 1.07117 kcal/mol@LB@@LB@Position - mRNA 155 -- 171@LB@Position - sRNA 26 -- 48@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 26 -- 32@LB@
90	0.01863	0.6177	b0659	ybeY	-9.29	0.057244	42 -- 51	47 -- 56	ssRNA-specific endoribonuclease; 16S rRNA 3' end maturation and quality control co-endoribonuclease working with RNase R; rRNA transcription antitermination factor	_____________41_________52\n_____________\|__________\|\n5'-ACU...GCCGA__________AUCAG...CGC-3'\n______________UGUCGAAGAG\n______________:\|\|\|:\|\|\|\|\|\n______________GCAGUUUCUC\n3'-UUU...ACCGG__________CUUAA...ACA-5'\n_____________\|__________\|\n_____________57_________46\n	45 -- 51	47 -- 53	-13.0692 kcal/mol	2.86289 kcal/mol	0.911734 kcal/mol	41 52@LB@ \| \|@LB@5'-ACU...GCCGA AUCAG...CGC-3'@LB@ UGUCGAAGAG@LB@ :\|\|\|:\|\|\|\|\|@LB@ GCAGUUUCUC@LB@3'-UUU...ACCGG CUUAA...ACA-5'@LB@ \| \|@LB@ 57 46@LB@@LB@@LB@Energy -9.29 kcal/mol@LB@Hybridization Energy -13.0692 kcal/mol@LB@Unfolding Energy - mRNA 2.86289 kcal/mol@LB@Unfolding Energy - sRNA 0.911734 kcal/mol@LB@@LB@Position - mRNA 42 -- 51@LB@Position - sRNA 47 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 47 -- 53@LB@
3	9.453e-06	0.01014	b0681	chiP	-16.40	0.001982	182 -- 193	45 -- 56	chitoporin uptake of chitosugars	_____________181__________194\n_____________\|____________\|\n5'-CUU...UUAUA____________UUAAC...AAG-3'\n______________CGUCAAAGAGGA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCUCCU\n3'-UUU...ACCGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	187 -- 193	45 -- 51	-19.4659 kcal/mol	2.1233 kcal/mol	0.938337 kcal/mol	181 194@LB@ \| \|@LB@5'-CUU...UUAUA UUAAC...AAG-3'@LB@ CGUCAAAGAGGA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCUCCU@LB@3'-UUU...ACCGG UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -19.4659 kcal/mol@LB@Unfolding Energy - mRNA 2.1233 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
144	0.02798	0.6177	b0682	chiQ	-9.70	0.047426	184 -- 197	41 -- 56	chitosugar-induced verified lipoprotein	_____________183______________198\n_____________\|________________\|\n5'-CGG...CCGCA____U___________GCUAU...ACA-3'\n______________CGUU___GAGGAAUUU\n______________\|\|\|:___\|\|\|\|\|\|\|\|\|\n______________GCAG___CUCCUUAAA\n3'-UUU...ACCGG____UUU_________GUAAA...ACA-5'\n_____________\|________________\|\n_____________57_______________40\n	191 -- 197	41 -- 47	-13.1137 kcal/mol	2.46147 kcal/mol	0.955312 kcal/mol	183 198@LB@ \| \|@LB@5'-CGG...CCGCA U GCUAU...ACA-3'@LB@ CGUU GAGGAAUUU@LB@ \|\|\|: \|\|\|\|\|\|\|\|\|@LB@ GCAG CUCCUUAAA@LB@3'-UUU...ACCGG UUU GUAAA...ACA-5'@LB@ \| \|@LB@ 57 40@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -13.1137 kcal/mol@LB@Unfolding Energy - mRNA 2.46147 kcal/mol@LB@Unfolding Energy - sRNA 0.955312 kcal/mol@LB@@LB@Position - mRNA 184 -- 197@LB@Position - sRNA 41 -- 56@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 41 -- 47@LB@
148	0.02945	0.6177	b0692	potE	-8.42	0.085901	187 -- 195	44 -- 52	putrescine/proton symporter: putrescine/ornithine antiporter	_____________186_______196\n_____________\|_________\|\n5'-UGU...UGUUG_________AAAUU...AGC-3'\n______________AAAGGGGAA\n______________\|\|\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-10.6161 kcal/mol	1.33649 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-UGU...UGUUG AAAUU...AGC-3'@LB@ AAAGGGGAA@LB@ \|\|\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -10.6161 kcal/mol@LB@Unfolding Energy - mRNA 1.33649 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
121	0.02422	0.6177	b0754	aroG	-7.67	0.121074	238 -- 245	47 -- 54	3-deoxy-D-arabino-heptulosonate-7-phosphate synthase phenylalanine repressible	_____________237______246\n_____________\|________\|\n5'-CUU...AGAAA________UUACU...CGA-3'\n______________UCAAAGAG\n______________\|\|\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	239 -- 245	47 -- 53	-9.80538 kcal/mol	1.24089 kcal/mol	0.897871 kcal/mol	237 246@LB@ \| \|@LB@5'-CUU...AGAAA UUACU...CGA-3'@LB@ UCAAAGAG@LB@ \|\|\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -9.80538 kcal/mol@LB@Unfolding Energy - mRNA 1.24089 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 238 -- 245@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 47 -- 53@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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