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
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@
178	0.03627	0.6177	b0924	mukB	-9.59	0.049840	186 -- 195	44 -- 53	chromosome condensin MukBEF ATPase and DNA-binding subunit	_____________185________196\n_____________\|__________\|\n5'-UGG...GAUAG__________GAAUA...CUG-3'\n______________CGGAGAGGAA\n______________\|::\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	44 -- 50	-13.8471 kcal/mol	3.32824 kcal/mol	0.927997 kcal/mol	185 196@LB@ \| \|@LB@5'-UGG...GAUAG GAAUA...CUG-3'@LB@ CGGAGAGGAA@LB@ \|::\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -13.8471 kcal/mol@LB@Unfolding Energy - mRNA 3.32824 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
4	0.0002658	0.2138	b1040	csgD	-11.06	0.024985	185 -- 199	38 -- 52	csgBAC operon transcriptional regulator	_____________184_____________200\n_____________\|_______________\|\n5'-UUA...UAAAA____C__________CAUGU...CGC-3'\n______________AAAG_GGGGUUUCAU\n______________\|\|\|\|_\|\|::\|\|\|\|\|\|\n______________UUUC_CCUUAAAGUA\n3'-UUU...GGCAG____U__________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	193 -- 199	38 -- 44	-14.3947 kcal/mol	2.26766 kcal/mol	1.0693 kcal/mol	184 200@LB@ \| \|@LB@5'-UUA...UAAAA C CAUGU...CGC-3'@LB@ AAAG GGGGUUUCAU@LB@ \|\|\|\| \|\|::\|\|\|\|\|\|@LB@ UUUC CCUUAAAGUA@LB@3'-UUU...GGCAG U AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -14.3947 kcal/mol@LB@Unfolding Energy - mRNA 2.26766 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 185 -- 199@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 38 -- 44@LB@
164	0.03346	0.6177	b1449	curA	-5.87	0.264423	114 -- 122	45 -- 53	curcumin/dihydrocurcumin reductase NADPH-dependent	_____________113_______123\n_____________\|_________\|\n5'-CGG...UGUUG_________UGUGA...UCG-3'\n______________CAGAGGGGA\n______________\|\|:\|\|:\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	116 -- 122	45 -- 51	-11.6619 kcal/mol	4.87234 kcal/mol	0.917553 kcal/mol	113 123@LB@ \| \|@LB@5'-CGG...UGUUG UGUGA...UCG-3'@LB@ CAGAGGGGA@LB@ \|\|:\|\|:\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -5.87 kcal/mol@LB@Hybridization Energy -11.6619 kcal/mol@LB@Unfolding Energy - mRNA 4.87234 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 114 -- 122@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 45 -- 51@LB@
150	0.03022	0.6177	b1285	gmr	-9.04	0.064446	208 -- 218	47 -- 57	cyclic-di-GMP phosphodiesterase; csgD regulator; modulator of RNase II stability	_____________207_________219\n_____________\|___________\|\n5'-UUU...GAAAA___________UCCAC...CUA-3'\n______________CCGUUAGGGAG\n______________\|\|\|\|:\|::\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	212 -- 218	47 -- 53	-14.7452 kcal/mol	2.96952 kcal/mol	2.73556 kcal/mol	207 219@LB@ \| \|@LB@5'-UUU...GAAAA UCCAC...CUA-3'@LB@ CCGUUAGGGAG@LB@ \|\|\|\|:\|::\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -14.7452 kcal/mol@LB@Unfolding Energy - mRNA 2.96952 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 208 -- 218@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 47 -- 53@LB@
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@
169	0.03425	0.6177	b0336	codB	-12.15	0.014930	188 -- 202	38 -- 52	cytosine transporter	_____________187_____________203\n_____________\|_______________\|\n5'-CCA...GCAAA_______________GUCGC...UUU-3'\n______________AAGGGGGAAUUUCGU\n______________\|\|:\|:\|\|\|\|\|\|\|\|:\|\n______________UUUCUCCUUAAAGUA\n3'-UUU...GGCAG_______________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	196 -- 202	38 -- 44	-18.3448 kcal/mol	5.13025 kcal/mol	1.0693 kcal/mol	187 203@LB@ \| \|@LB@5'-CCA...GCAAA GUCGC...UUU-3'@LB@ AAGGGGGAAUUUCGU@LB@ \|\|:\|:\|\|\|\|\|\|\|\|:\|@LB@ UUUCUCCUUAAAGUA@LB@3'-UUU...GGCAG AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -18.3448 kcal/mol@LB@Unfolding Energy - mRNA 5.13025 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 188 -- 202@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
157	0.03134	0.6177	b4086	alsC	-8.98	0.066369	183 -- 191	45 -- 53	D-allose ABC transporter permease	_____________182_______192\n_____________\|_________\|\n5'-CGC...AUGAG_________GAUUA...CGA-3'\n______________CGAAGAGGA\n______________\|:\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	185 -- 191	45 -- 51	-13.528 kcal/mol	3.63363 kcal/mol	0.917553 kcal/mol	182 192@LB@ \| \|@LB@5'-CGC...AUGAG GAUUA...CGA-3'@LB@ CGAAGAGGA@LB@ \|:\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -13.528 kcal/mol@LB@Unfolding Energy - mRNA 3.63363 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 183 -- 191@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 185 -- 191@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)

Job resubmission

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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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