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
22	0.004195	0.5992	b3715	yieH	-7.44	0.134211	287 -- 299	41 -- 55	phosphoenolpyruvate and 6-phosphogluconate phosphatase	_____________286_____________300\n_____________\|_______________\|\n5'-CUG...ACGAU___UC__________G-3'\n______________GUU____AGGAAUUU\n______________\|\|:____\|\|\|\|\|\|\|\|\n______________CAG____UCCUUAAA\n3'-UUU...CCGGG___UUUC________GUAAA...ACA-5'\n_____________\|_______________\|\n_____________56______________40\n	293 -- 299	41 -- 47	-8.9861 kcal/mol	0.60049 kcal/mol	0.947844 kcal/mol	286 300@LB@ \| \|@LB@5'-CUG...ACGAU UC G-3'@LB@ GUU AGGAAUUU@LB@ \|\|: \|\|\|\|\|\|\|\|@LB@ CAG UCCUUAAA@LB@3'-UUU...CCGGG UUUC GUAAA...ACA-5'@LB@ \| \|@LB@ 56 40@LB@@LB@@LB@Energy -7.44 kcal/mol@LB@Hybridization Energy -8.9861 kcal/mol@LB@Unfolding Energy - mRNA 0.60049 kcal/mol@LB@Unfolding Energy - sRNA 0.947844 kcal/mol@LB@@LB@Position - mRNA 287 -- 299@LB@Position - sRNA 41 -- 55@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 41 -- 47@LB@
68	0.01422	0.6177	b3826	yigL	-7.04	0.159921	44 -- 50	49 -- 55	pyridoxal phosphate phosphatase	_____________43______51\n_____________\|_______\|\n5'-GCA...AUCCU_______GAGGA...CGC-3'\n______________GUCGAAG\n______________\|\|\|:\|\|\|\n______________CAGUUUC\n3'-UUU...CCGGG_______UCCUU...ACA-5'\n_____________\|_______\|\n_____________56______48\n	44 -- 50	49 -- 55	-7.68974 kcal/mol	0.331193 kcal/mol	0.314364 kcal/mol	43 51@LB@ \| \|@LB@5'-GCA...AUCCU GAGGA...CGC-3'@LB@ GUCGAAG@LB@ \|\|\|:\|\|\|@LB@ CAGUUUC@LB@3'-UUU...CCGGG UCCUU...ACA-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -7.68974 kcal/mol@LB@Unfolding Energy - mRNA 0.331193 kcal/mol@LB@Unfolding Energy - sRNA 0.314364 kcal/mol@LB@@LB@Position - mRNA 44 -- 50@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 49 -- 55@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@
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@
153	0.03061	0.6177	b4060	yjcB	-6.94	0.167417	88 -- 108	29 -- 50	putative inner membrane protein	_____________87_____________________109\n_____________\|______________________\|\n5'-AUA...CAAAC____U____________G____CUGCA...GGU-3'\n______________AGAG__GUUUCAUUUUU_UGUU\n______________\|\|\|\|__:\|\|\|\|\|\|\|\|\|\|_\|:\|\|\n______________UCUC__UAAAGUAAAAA_AUAA\n3'-UUU...CAGUU____CU___________A____UAAUA...ACA-5'\n_____________\|______________________\|\n_____________51_____________________28\n	97 -- 103	34 -- 40	-13.8913 kcal/mol	5.87088 kcal/mol	1.08007 kcal/mol	87 109@LB@ \| \|@LB@5'-AUA...CAAAC U G CUGCA...GGU-3'@LB@ AGAG GUUUCAUUUUU UGUU@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|\|\| \|:\|\|@LB@ UCUC UAAAGUAAAAA AUAA@LB@3'-UUU...CAGUU CU A UAAUA...ACA-5'@LB@ \| \|@LB@ 51 28@LB@@LB@@LB@Energy -6.94 kcal/mol@LB@Hybridization Energy -13.8913 kcal/mol@LB@Unfolding Energy - mRNA 5.87088 kcal/mol@LB@Unfolding Energy - sRNA 1.08007 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 29 -- 50@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 34 -- 40@LB@
37	0.007616	0.6129	b4141	yjeH	-11.12	0.024259	30 -- 40	44 -- 54	putative transporter	_____________29__________41\n_____________\|___________\|\n5'-CAG...CCCCU___________AAAGA...CUG-3'\n______________UCAAGGGGGAA\n______________\|\|\|\|:\|:\|\|\|\|\n______________AGUUUCUCCUU\n3'-UUU...CGGGC___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	34 -- 40	44 -- 50	-14.4219 kcal/mol	2.36204 kcal/mol	0.939671 kcal/mol	29 41@LB@ \| \|@LB@5'-CAG...CCCCU AAAGA...CUG-3'@LB@ UCAAGGGGGAA@LB@ \|\|\|\|:\|:\|\|\|\|@LB@ AGUUUCUCCUU@LB@3'-UUU...CGGGC AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.4219 kcal/mol@LB@Unfolding Energy - mRNA 2.36204 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 30 -- 40@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 44 -- 50@LB@
34	0.007003	0.6129	b4199	yjfY	-12.43	0.013073	184 -- 195	46 -- 57	YhcN family protein periplasmic	_____________183__________196\n_____________\|____________\|\n5'-AGG...GUCAG____________UAUCU...ACG-3'\n______________CCGUCGAGGAGG\n______________\|\|\|\|\|:\|:\|\|\|\|\n______________GGCAGUUUCUCC\n3'-UUU...AACCG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	189 -- 195	46 -- 52	-19.9606 kcal/mol	4.79886 kcal/mol	2.7365 kcal/mol	183 196@LB@ \| \|@LB@5'-AGG...GUCAG UAUCU...ACG-3'@LB@ CCGUCGAGGAGG@LB@ \|\|\|\|\|:\|:\|\|\|\|@LB@ GGCAGUUUCUCC@LB@3'-UUU...AACCG UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -12.43 kcal/mol@LB@Hybridization Energy -19.9606 kcal/mol@LB@Unfolding Energy - mRNA 4.79886 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@LB@
191	0.0398	0.6177	b4335	yjiM	-5.72	0.281824	283 -- 290	47 -- 54	putative 2-hydroxyglutaryl-CoA dehydratase	_____________282______291\n_____________\|________\|\n5'-CGG...GGAUC________CGCGG...UUC-3'\n______________UCAAGGAG\n______________\|\|\|\|:\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	284 -- 290	47 -- 53	-8.85878 kcal/mol	2.24401 kcal/mol	0.897871 kcal/mol	282 291@LB@ \| \|@LB@5'-CGG...GGAUC CGCGG...UUC-3'@LB@ UCAAGGAG@LB@ \|\|\|\|:\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -5.72 kcal/mol@LB@Hybridization Energy -8.85878 kcal/mol@LB@Unfolding Energy - mRNA 2.24401 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 283 -- 290@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 47 -- 53@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@
130	0.02541	0.6177	b4365	yjjQ	-8.08	0.100207	263 -- 277	38 -- 55	putative transcriptional regulator	_____________262_________________278\n_____________\|___________________\|\n5'-AGG...GCAGG___A_______________GAGGA...AUG-3'\n______________GUU_AAAGAGG____UCAU\n______________\|\|:_\|\|\|\|\|\|\|____\|\|\|\|\n______________CAG_UUUCUCC____AGUA\n3'-UUU...CCGGG___________UUAA____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	267 -- 273	46 -- 52	-10.7142 kcal/mol	1.46087 kcal/mol	1.17036 kcal/mol	262 278@LB@ \| \|@LB@5'-AGG...GCAGG A GAGGA...AUG-3'@LB@ GUU AAAGAGG UCAU@LB@ \|\|: \|\|\|\|\|\|\| \|\|\|\|@LB@ CAG UUUCUCC AGUA@LB@3'-UUU...CCGGG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -10.7142 kcal/mol@LB@Unfolding Energy - mRNA 1.46087 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 46 -- 52@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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