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
96	0.01897	0.6177	b2422	cysA	-7.76	0.115977	190 -- 202	38 -- 50	sulfate/thiosulfate transporter subunit		_____________189___________203\n_____________\|_____________\|\n5'-GGU...CAGCA_______CA____GAGCA...UGC-3'\n______________GGAGGAA__UCAU\n______________:\|\|\|\|\|\|__\|\|\|\|\n______________UCUCCUU__AGUA\n3'-UUU...CAGUU_______AA____AAAAA...ACA-5'\n_____________\|_____________\|\n_____________51____________37\n	190 -- 196	44 -- 50	-11.8687 kcal/mol	3.04673 kcal/mol	1.0603 kcal/mol	189 203@LB@ \| \|@LB@5'-GGU...CAGCA CA GAGCA...UGC-3'@LB@ GGAGGAA UCAU@LB@ :\|\|\|\|\|\| \|\|\|\|@LB@ UCUCCUU AGUA@LB@3'-UUU...CAGUU AA AAAAA...ACA-5'@LB@ \| \|@LB@ 51 37@LB@@LB@@LB@Energy -7.76 kcal/mol@LB@Hybridization Energy -11.8687 kcal/mol@LB@Unfolding Energy - mRNA 3.04673 kcal/mol@LB@Unfolding Energy - sRNA 1.0603 kcal/mol@LB@@LB@Position - mRNA 190 -- 202@LB@Position - sRNA 38 -- 50@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
200	0.04173	0.6177	b3155	yhbQ	-7.74	0.117248	9 -- 16	50 -- 57	GIY-YIG nuclease superfamily protein		_____________8________17\n_____________\|________\|\n___5'-UUUUUCUU________AUGUA...GCG-3'\n______________CCGUCAAA\n______________\|\|\|\|\|\|\|\|\n______________GGCAGUUU\n3'-UUU...AACCG________CUCCU...ACA-5'\n_____________\|________\|\n_____________58_______49\n	10 -- 16	50 -- 56	-10.5697 kcal/mol	0.110673 kcal/mol	2.72137 kcal/mol	8 17@LB@ \| \|@LB@ 5'-UUUUUCUU AUGUA...GCG-3'@LB@ CCGUCAAA@LB@ \|\|\|\|\|\|\|\|@LB@ GGCAGUUU@LB@3'-UUU...AACCG CUCCU...ACA-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -10.5697 kcal/mol@LB@Unfolding Energy - mRNA 0.110673 kcal/mol@LB@Unfolding Energy - sRNA 2.72137 kcal/mol@LB@@LB@Position - mRNA 9 -- 16@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 50 -- 56@LB@
167	0.03387	0.6177	b3980	tufB	-7.70	0.119070	183 -- 194	44 -- 55	translation elongation factor EF-Tu 2	b3339	_____________182__________195\n_____________\|____________\|\n5'-UCC...UCCGU___UU_______CAAUC...CUA-3'\n______________GUC__AGAGGGA\n______________\|\|\|__\|\|\|\|\|:\|\n______________CAG__UCUCCUU\n3'-UUU...CCGGG___UU_______AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	188 -- 194	44 -- 50	-14.3886 kcal/mol	5.74361 kcal/mol	0.941432 kcal/mol	182 195@LB@ \| \|@LB@5'-UCC...UCCGU UU CAAUC...CUA-3'@LB@ GUC AGAGGGA@LB@ \|\|\| \|\|\|\|\|:\|@LB@ CAG UCUCCUU@LB@3'-UUU...CCGGG UU AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.70 kcal/mol@LB@Hybridization Energy -14.3886 kcal/mol@LB@Unfolding Energy - mRNA 5.74361 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 188 -- 194@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@
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@
159	0.0318	0.6177	b2532	trmJ	-7.64	0.122614	101 -- 114	44 -- 55	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent		_____________100____________115\n_____________\|______________\|\n5'-CGU...UGGAU________AC____AAACG...UGU-3'\n______________GUUAAAGA__GGGA\n______________\|\|:\|\|\|\|\|__\|\|:\|\n______________CAGUUUCU__CCUU\n3'-UUU...CCGGG______________AAAGU...ACA-5'\n_____________\|______________\|\n_____________56_____________43\n	102 -- 108	48 -- 54	-10.9175 kcal/mol	2.33739 kcal/mol	0.941432 kcal/mol	100 115@LB@ \| \|@LB@5'-CGU...UGGAU AC AAACG...UGU-3'@LB@ GUUAAAGA GGGA@LB@ \|\|:\|\|\|\|\| \|\|:\|@LB@ CAGUUUCU CCUU@LB@3'-UUU...CCGGG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -10.9175 kcal/mol@LB@Unfolding Energy - mRNA 2.33739 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 101 -- 114@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 48 -- 54@LB@
183	0.03803	0.6177	b3616	tdh	-7.63	0.122830	33 -- 50	37 -- 52	L-threonine 3-dehydrogenase NAD(P)-binding		_____________32_________________51\n_____________\|__________________\|\n5'-UAG...UGCAA________C____A____ACCGG...GUA-3'\n______________AAAGAGGG_AUUU_CGUU\n______________\|\|\|\|\|\|\|:_\|\|\|\|_\|:\|\|\n______________UUUCUCCU_UAAA_GUAA\n3'-UUU...GGCAG__________________AAAAA...ACA-5'\n_____________\|__________________\|\n_____________53_________________36\n	34 -- 40	45 -- 51	-11.8553 kcal/mol	3.14412 kcal/mol	1.07641 kcal/mol	32 51@LB@ \| \|@LB@5'-UAG...UGCAA C A ACCGG...GUA-3'@LB@ AAAGAGGG AUUU CGUU@LB@ \|\|\|\|\|\|\|: \|\|\|\| \|:\|\|@LB@ UUUCUCCU UAAA GUAA@LB@3'-UUU...GGCAG AAAAA...ACA-5'@LB@ \| \|@LB@ 53 36@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -11.8553 kcal/mol@LB@Unfolding Energy - mRNA 3.14412 kcal/mol@LB@Unfolding Energy - sRNA 1.07641 kcal/mol@LB@@LB@Position - mRNA 33 -- 50@LB@Position - sRNA 37 -- 52@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 45 -- 51@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@
122	0.02427	0.6177	b1116	lolC	-7.56	0.127136	206 -- 233	55 -- 74	lipoprotein-releasing system transmembrane protein		_____________205__________________________234\n_____________\|____________________________\|\n5'-GUA...AUGUA____CC_______CUAUUU_________CGUUA...GCA-3'\n______________CCAA__UGUCGCU______AUUGGCCUG\n______________\|\|\|\|__\|:\|\|\|\|\|______\|\|\|\|\|\|\|:\|\n______________GGUU__AUAGCGA______UAACCGGGC\n3'-UUU...UUACC____________________________AGUUU...ACA-5'\n_____________\|____________________________\|\n_____________75___________________________54\n	212 -- 218	64 -- 70	-24.394 kcal/mol	5.52374 kcal/mol	11.3119 kcal/mol	205 234@LB@ \| \|@LB@5'-GUA...AUGUA CC CUAUUU CGUUA...GCA-3'@LB@ CCAA UGUCGCU AUUGGCCUG@LB@ \|\|\|\| \|:\|\|\|\|\| \|\|\|\|\|\|\|:\|@LB@ GGUU AUAGCGA UAACCGGGC@LB@3'-UUU...UUACC AGUUU...ACA-5'@LB@ \| \|@LB@ 75 54@LB@@LB@@LB@Energy -7.56 kcal/mol@LB@Hybridization Energy -24.394 kcal/mol@LB@Unfolding Energy - mRNA 5.52374 kcal/mol@LB@Unfolding Energy - sRNA 11.3119 kcal/mol@LB@@LB@Position - mRNA 206 -- 233@LB@Position - sRNA 55 -- 74@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 64 -- 70@LB@
113	0.02257	0.6177	b0915	lpxK	-7.55	0.127690	105 -- 116	46 -- 56	lipid A 4'kinase		_____________104__________117\n_____________\|____________\|\n5'-GAA...GUGGU_________U__UGUCA...GCU-3'\n______________CGUCGAGGA_GG\n______________\|\|\|\|:\|:\|\|_\|\|\n______________GCAGUUUCU_CC\n3'-UUU...ACCGG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________57___________45\n	107 -- 113	48 -- 54	-12.734 kcal/mol	4.25329 kcal/mol	0.93204 kcal/mol	104 117@LB@ \| \|@LB@5'-GAA...GUGGU U UGUCA...GCU-3'@LB@ CGUCGAGGA GG@LB@ \|\|\|\|:\|:\|\| \|\|@LB@ GCAGUUUCU CC@LB@3'-UUU...ACCGG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -7.55 kcal/mol@LB@Hybridization Energy -12.734 kcal/mol@LB@Unfolding Energy - mRNA 4.25329 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 105 -- 116@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 48 -- 54@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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