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
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@
172	0.03476	0.6177	b3441	yhhY	-9.34	0.055938	185 -- 193	45 -- 53	aminoacyl nucleotide detoxifying acetyltransferase		_____________184_______194\n_____________\|_________\|\n5'-CCC...UACCC_________CAAAG...UGC-3'\n______________CAAAGAGGA\n______________\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	187 -- 193	45 -- 51	-12.8083 kcal/mol	2.54681 kcal/mol	0.917553 kcal/mol	184 194@LB@ \| \|@LB@5'-CCC...UACCC CAAAG...UGC-3'@LB@ CAAAGAGGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -12.8083 kcal/mol@LB@Unfolding Energy - mRNA 2.54681 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 185 -- 193@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
173	0.03478	0.6177	b1234	rssA	-4.70	0.418234	181 -- 188	43 -- 50	putative patatin-like family phospholipase		_____________180______189\n_____________\|________\|\n5'-GAU...AUUCC________CUUGC...AAA-3'\n______________AGGGGAAU\n______________\|\|:\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	182 -- 188	43 -- 49	-9.05148 kcal/mol	3.5051 kcal/mol	0.845564 kcal/mol	180 189@LB@ \| \|@LB@5'-GAU...AUUCC CUUGC...AAA-3'@LB@ AGGGGAAU@LB@ \|\|:\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -4.70 kcal/mol@LB@Hybridization Energy -9.05148 kcal/mol@LB@Unfolding Energy - mRNA 3.5051 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 181 -- 188@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 43 -- 49@LB@
174	0.03548	0.6177	b2437	eutR	-7.66	0.121193	279 -- 299	38 -- 55	eut operon transcriptional activator AraC family		_____________278___________________300\n_____________\|_____________________\|\n5'-CGC...CGAAG_______U___UAAUG_____C-3'\n______________GUCGAAG_GGA_____UUCAU\n______________\|\|\|:\|\|\|_\|\|\|_____\|\|\|\|\|\n______________CAGUUUC_CCU_____AAGUA\n3'-UUU...CCGGG_______U___UA________AAAAA...ACA-5'\n_____________\|_____________________\|\n_____________56____________________37\n	279 -- 285	49 -- 55	-15.2982 kcal/mol	6.46344 kcal/mol	1.17036 kcal/mol	278 300@LB@ \| \|@LB@5'-CGC...CGAAG U UAAUG C-3'@LB@ GUCGAAG GGA UUCAU@LB@ \|\|\|:\|\|\| \|\|\| \|\|\|\|\|@LB@ CAGUUUC CCU AAGUA@LB@3'-UUU...CCGGG U UA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -15.2982 kcal/mol@LB@Unfolding Energy - mRNA 6.46344 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 279 -- 299@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 49 -- 55@LB@
175	0.03585	0.6177	b2028	ugd	-9.30	0.056993	217 -- 248	46 -- 74	UDP-glucose 6-dehydrogenase		_____________216______________________________249\n_____________\|________________________________\|\n5'-GCU...CAUUU______C_G_____GUA___________C___CUUCU...CAC-3'\n______________CCGGUA_U_GCUAU___GGCUUGUCAAA_GGG\n______________\|\|::\|\|_\|_\|\|\|\|\|___\|\|\|::\|\|\|\|\|\|_:\|\|\n______________GGUUAU_A_CGAUA___CCGGGCAGUUU_UCC\n3'-UUU...UUACC________G_____A_____________C___UUAAA...ACA-5'\n_____________\|________________________________\|\n_____________75_______________________________45\n	238 -- 244	50 -- 56	-30.8605 kcal/mol	10.2215 kcal/mol	11.335 kcal/mol	216 249@LB@ \| \|@LB@5'-GCU...CAUUU C G GUA C CUUCU...CAC-3'@LB@ CCGGUA U GCUAU GGCUUGUCAAA GGG@LB@ \|\|::\|\| \| \|\|\|\|\| \|\|\|::\|\|\|\|\|\| :\|\|@LB@ GGUUAU A CGAUA CCGGGCAGUUU UCC@LB@3'-UUU...UUACC G A C UUAAA...ACA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -30.8605 kcal/mol@LB@Unfolding Energy - mRNA 10.2215 kcal/mol@LB@Unfolding Energy - sRNA 11.335 kcal/mol@LB@@LB@Position - mRNA 217 -- 248@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 50 -- 56@LB@
176	0.03596	0.6177	b1747	astA	-4.82	0.399998	129 -- 139	46 -- 56	arginine succinyltransferase		_____________128_________140\n_____________\|___________\|\n5'-GGC...GUCAG__AA_______UGACG...AAG-3'\n______________CG__GAAGAGG\n______________\|\|__:\|\|\|\|\|\|\n______________GC__UUUCUCC\n3'-UUU...ACCGG__AG_______UUAAA...ACA-5'\n_____________\|___________\|\n_____________57__________45\n	133 -- 139	46 -- 52	-9.86744 kcal/mol	4.11365 kcal/mol	0.93204 kcal/mol	128 140@LB@ \| \|@LB@5'-GGC...GUCAG AA UGACG...AAG-3'@LB@ CG GAAGAGG@LB@ \|\| :\|\|\|\|\|\|@LB@ GC UUUCUCC@LB@3'-UUU...ACCGG AG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -4.82 kcal/mol@LB@Hybridization Energy -9.86744 kcal/mol@LB@Unfolding Energy - mRNA 4.11365 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 129 -- 139@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 46 -- 52@LB@
177	0.03616	0.6177	b1474	fdnG	-8.74	0.074199	188 -- 196	44 -- 52	formate dehydrogenase-N alpha subunit nitrate-inducible	b3894	_____________187_______197\n_____________\|_________\|\n5'-AUU...UGAAA_________AGCAA...CUC-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	190 -- 196	44 -- 50	-11.3772 kcal/mol	1.78024 kcal/mol	0.860683 kcal/mol	187 197@LB@ \| \|@LB@5'-AUU...UGAAA AGCAA...CUC-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -11.3772 kcal/mol@LB@Unfolding Energy - mRNA 1.78024 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@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@
179	0.03684	0.6177	b0335	prpE	-7.81	0.113441	203 -- 221	38 -- 55	propionate--CoA ligase		_____________202_________________222\n_____________\|___________________\|\n5'-GCC...AUUAU___UUUU__C_________CAGCG...AAA-3'\n______________GUC____AG_GAAUUUUAU\n______________\|\|\|____\|\|_\|\|\|\|\|\|:\|\|\n______________CAG____UC_CUUAAAGUA\n3'-UUU...CCGGG___UUUC____________AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	215 -- 221	38 -- 44	-10.8576 kcal/mol	1.87676 kcal/mol	1.17036 kcal/mol	202 222@LB@ \| \|@LB@5'-GCC...AUUAU UUUU C CAGCG...AAA-3'@LB@ GUC AG GAAUUUUAU@LB@ \|\|\| \|\| \|\|\|\|\|\|:\|\|@LB@ CAG UC CUUAAAGUA@LB@3'-UUU...CCGGG UUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -10.8576 kcal/mol@LB@Unfolding Energy - mRNA 1.87676 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
180	0.03697	0.6177	b1325	ycjG	-6.24	0.226397	189 -- 195	47 -- 53	L-Ala-D/L-Glu epimerase		_____________188_____196\n_____________\|_______\|\n5'-AAG...GACAA_______UAAAG...AAC-3'\n______________CAAGGAG\n______________\|\|\|:\|\|\|\n______________GUUUCUC\n3'-UUU...GGGCA_______CUUAA...ACA-5'\n_____________\|_______\|\n_____________54______46\n	189 -- 195	47 -- 53	-8.11062 kcal/mol	0.981925 kcal/mol	0.886139 kcal/mol	188 196@LB@ \| \|@LB@5'-AAG...GACAA UAAAG...AAC-3'@LB@ CAAGGAG@LB@ \|\|\|:\|\|\|@LB@ GUUUCUC@LB@3'-UUU...GGGCA CUUAA...ACA-5'@LB@ \| \|@LB@ 54 46@LB@@LB@@LB@Energy -6.24 kcal/mol@LB@Hybridization Energy -8.11062 kcal/mol@LB@Unfolding Energy - mRNA 0.981925 kcal/mol@LB@Unfolding Energy - sRNA 0.886139 kcal/mol@LB@@LB@Position - mRNA 189 -- 195@LB@Position - sRNA 47 -- 53@LB@Position Seed - mRNA 189 -- 195@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching