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	Additional homologs
146	0.02871	0.6177	b1120	cobB	-8.56	0.080407	32 -- 40	43 -- 51	deacetylase of acs and cheY chemotaxis regulator		_____________31________41\n_____________\|_________\|\n5'-CGC...GAUGC_________GCGUG...AUC-3'\n______________GGGAGGAAU\n______________::\|\|\|\|\|\|\|\n______________UUCUCCUUA\n3'-UUU...GCAGU_________AAGUA...ACA-5'\n_____________\|_________\|\n_____________52________42\n	34 -- 40	43 -- 49	-11.3695 kcal/mol	1.94725 kcal/mol	0.859837 kcal/mol	31 41@LB@ \| \|@LB@5'-CGC...GAUGC GCGUG...AUC-3'@LB@ GGGAGGAAU@LB@ ::\|\|\|\|\|\|\|@LB@ UUCUCCUUA@LB@3'-UUU...GCAGU AAGUA...ACA-5'@LB@ \| \|@LB@ 52 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -11.3695 kcal/mol@LB@Unfolding Energy - mRNA 1.94725 kcal/mol@LB@Unfolding Energy - sRNA 0.859837 kcal/mol@LB@@LB@Position - mRNA 32 -- 40@LB@Position - sRNA 43 -- 51@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 43 -- 49@LB@
171	0.0346	0.6177	b1865	nudB	-7.50	0.130652	189 -- 196	46 -- 53	dihydroneopterin triphosphate pyrophosphatase		_____________188______197\n_____________\|________\|\n5'-UGA...GUCAA________CAGCG...CCG-3'\n______________CGAAGAGG\n______________\|:\|\|\|\|\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	190 -- 196	46 -- 52	-10.7995 kcal/mol	2.39118 kcal/mol	0.910679 kcal/mol	188 197@LB@ \| \|@LB@5'-UGA...GUCAA CAGCG...CCG-3'@LB@ CGAAGAGG@LB@ \|:\|\|\|\|\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -10.7995 kcal/mol@LB@Unfolding Energy - mRNA 2.39118 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 189 -- 196@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 46 -- 52@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@
111	0.02245	0.6177	b3413	gntX	-10.38	0.034336	253 -- 267	41 -- 55	DNA catabolic protein		_____________252_____________268\n_____________\|_______________\|\n5'-CCC...GUUAG____UU_________GUUCG...AUA-3'\n______________GUCA__GGGGGAUUU\n______________\|\|\|\|__\|:\|\|:\|\|\|\|\n______________CAGU__CUCCUUAAA\n3'-UUU...CCGGG____UU_________GUAAA...ACA-5'\n_____________\|_______________\|\n_____________56______________40\n	261 -- 267	41 -- 47	-16.783 kcal/mol	5.45091 kcal/mol	0.947844 kcal/mol	252 268@LB@ \| \|@LB@5'-CCC...GUUAG UU GUUCG...AUA-3'@LB@ GUCA GGGGGAUUU@LB@ \|\|\|\| \|:\|\|:\|\|\|\|@LB@ CAGU CUCCUUAAA@LB@3'-UUU...CCGGG UU GUAAA...ACA-5'@LB@ \| \|@LB@ 56 40@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -16.783 kcal/mol@LB@Unfolding Energy - mRNA 5.45091 kcal/mol@LB@Unfolding Energy - sRNA 0.947844 kcal/mol@LB@@LB@Position - mRNA 253 -- 267@LB@Position - sRNA 41 -- 55@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 41 -- 47@LB@
184	0.03803	0.6177	b3647	ligB	-3.67	0.590336	72 -- 111	39 -- 67	DNA ligase NAD(+)-dependent		_____________71________________________________________112\n_____________\|_________________________________________\|\n5'-GGC...GCUUC_______U________UUCACUGCAAUA____C__U_____GGAAG...AAA-3'\n______________CGC_AUU_GCCUGUCA____________AAGA_GA_UUUCA\n______________\|\|\|_\|\|\|_\|\|\|:\|\|\|\|____________\|\|\|\|_\|\|_\|\|\|\|\|\n______________GCG_UAA_CGGGCAGU____________UUCU_CU_AAAGU\n3'-UUU...UUAUA___A___C________________________C__U_____AAAAA...ACA-5'\n_____________\|_________________________________________\|\n_____________68________________________________________38\n	80 -- 86	52 -- 58	-24.1741 kcal/mol	6.974 kcal/mol	13.5271 kcal/mol	71 112@LB@ \| \|@LB@5'-GGC...GCUUC U UUCACUGCAAUA C U GGAAG...AAA-3'@LB@ CGC AUU GCCUGUCA AAGA GA UUUCA@LB@ \|\|\| \|\|\| \|\|\|:\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|@LB@ GCG UAA CGGGCAGU UUCU CU AAAGU@LB@3'-UUU...UUAUA A C C U AAAAA...ACA-5'@LB@ \| \|@LB@ 68 38@LB@@LB@@LB@Energy -3.67 kcal/mol@LB@Hybridization Energy -24.1741 kcal/mol@LB@Unfolding Energy - mRNA 6.974 kcal/mol@LB@Unfolding Energy - sRNA 13.5271 kcal/mol@LB@@LB@Position - mRNA 72 -- 111@LB@Position - sRNA 39 -- 67@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 52 -- 58@LB@
168	0.03398	0.6177	b0321	yahG	-8.56	0.080369	183 -- 192	44 -- 53	DUF1116 family protein	b4572	_____________182________193\n_____________\|__________\|\n5'-AUC...AUCUG__________GAAGC...AAC-3'\n______________CAAAGGGGAG\n______________\|\|\|\|\|:\|\|\|:\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	186 -- 192	44 -- 50	-12.9704 kcal/mol	3.47901 kcal/mol	0.927997 kcal/mol	182 193@LB@ \| \|@LB@5'-AUC...AUCUG GAAGC...AAC-3'@LB@ CAAAGGGGAG@LB@ \|\|\|\|\|:\|\|\|:@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -12.9704 kcal/mol@LB@Unfolding Energy - mRNA 3.47901 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 183 -- 192@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 44 -- 50@LB@
126	0.02445	0.6177	b4364	yjjP	-5.95	0.256190	188 -- 200	42 -- 53	DUF1212 family inner membrane protein		_____________187___________201\n_____________\|_____________\|\n5'-UCA...UAUGA_______C_____AUGCA...UUU-3'\n______________CAAAGGG_GAGUU\n______________\|\|\|\|\|:\|_\|\|:\|\|\n______________GUUUCUC_CUUAA\n3'-UUU...GGGCA_____________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________54____________41\n	188 -- 194	47 -- 53	-11.6429 kcal/mol	4.76073 kcal/mol	0.933904 kcal/mol	187 201@LB@ \| \|@LB@5'-UCA...UAUGA C AUGCA...UUU-3'@LB@ CAAAGGG GAGUU@LB@ \|\|\|\|\|:\| \|\|:\|\|@LB@ GUUUCUC CUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -5.95 kcal/mol@LB@Hybridization Energy -11.6429 kcal/mol@LB@Unfolding Energy - mRNA 4.76073 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 188 -- 200@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 47 -- 53@LB@
48	0.00943	0.6129	b3033	yqiB	-8.72	0.074798	113 -- 121	44 -- 52	DUF1249 protein YqiB		_____________112_______122\n_____________\|_________\|\n5'-UGG...GUAGA_________AAUCG...GCG-3'\n______________AGAGGGGAA\n______________\|:\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	115 -- 121	44 -- 50	-10.7393 kcal/mol	1.15971 kcal/mol	0.860683 kcal/mol	112 122@LB@ \| \|@LB@5'-UGG...GUAGA AAUCG...GCG-3'@LB@ AGAGGGGAA@LB@ \|:\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.15971 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 113 -- 121@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 44 -- 50@LB@
100	0.01963	0.6177	b4001	yjaH	-9.93	0.042585	215 -- 230	39 -- 53	DUF1481 family putative lipoprotein		_____________214______________231\n_____________\|________________\|\n5'-UGG...UUUAA________U_______CCCCU...AUA-3'\n______________CGAAGGGG_GGUUUCA\n______________\|:\|\|\|:\|\|_::\|\|\|\|\|\n______________GUUUCUCC_UUAAAGU\n3'-UUU...GGGCA________________AAAAA...ACA-5'\n_____________\|________________\|\n_____________54_______________38\n	216 -- 222	46 -- 52	-15.2589 kcal/mol	4.19806 kcal/mol	1.13439 kcal/mol	214 231@LB@ \| \|@LB@5'-UGG...UUUAA U CCCCU...AUA-3'@LB@ CGAAGGGG GGUUUCA@LB@ \|:\|\|\|:\|\| ::\|\|\|\|\|@LB@ GUUUCUCC UUAAAGU@LB@3'-UUU...GGGCA AAAAA...ACA-5'@LB@ \| \|@LB@ 54 38@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -15.2589 kcal/mol@LB@Unfolding Energy - mRNA 4.19806 kcal/mol@LB@Unfolding Energy - sRNA 1.13439 kcal/mol@LB@@LB@Position - mRNA 215 -- 230@LB@Position - sRNA 39 -- 53@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 46 -- 52@LB@
77	0.01626	0.6177	b1414	ydcF	-7.59	0.125301	189 -- 198	44 -- 53	DUF218 superfamily protein SAM-binding		_____________188________199\n_____________\|__________\|\n5'-GGU...AACGA__________CCAUG...UGC-3'\n______________UAAGGAGGAA\n______________:\|\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	192 -- 198	44 -- 50	-11.4771 kcal/mol	2.95852 kcal/mol	0.927997 kcal/mol	188 199@LB@ \| \|@LB@5'-GGU...AACGA CCAUG...UGC-3'@LB@ UAAGGAGGAA@LB@ :\|\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -7.59 kcal/mol@LB@Hybridization Energy -11.4771 kcal/mol@LB@Unfolding Energy - mRNA 2.95852 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 189 -- 198@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@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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