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
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@
42	0.008125	0.6129	b2431	yfeX	-9.88	0.043594	266 -- 278	44 -- 56	porphyrinogen oxidase cytoplasmic	_____________265___________279\n_____________\|_____________\|\n5'-AUU...GCCAA___G_________GUUGA...CCA-3'\n______________CGU_AAAGGGGAA\n______________\|\|\|_\|\|\|\|:\|\|\|\|\n______________GCA_UUUCUCCUU\n3'-UUU...ACCGG___G_________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________57____________43\n	272 -- 278	44 -- 50	-15.4775 kcal/mol	4.65199 kcal/mol	0.948902 kcal/mol	265 279@LB@ \| \|@LB@5'-AUU...GCCAA G GUUGA...CCA-3'@LB@ CGU AAAGGGGAA@LB@ \|\|\| \|\|\|\|:\|\|\|\|@LB@ GCA UUUCUCCUU@LB@3'-UUU...ACCGG G AAAGU...ACA-5'@LB@ \| \|@LB@ 57 43@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -15.4775 kcal/mol@LB@Unfolding Energy - mRNA 4.65199 kcal/mol@LB@Unfolding Energy - sRNA 0.948902 kcal/mol@LB@@LB@Position - mRNA 266 -- 278@LB@Position - sRNA 44 -- 56@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 44 -- 50@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@
83	0.0176	0.6177	b2457	eutM	-9.48	0.052376	185 -- 194	44 -- 53	ethanolamine utilization protein putative carboxysome structural protein	_____________184________195\n_____________\|__________\|\n5'-UAU...CCUGA__________AGCAC...UUA-3'\n______________UAAAGAGGAA\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	188 -- 194	44 -- 50	-11.8586 kcal/mol	1.44575 kcal/mol	0.927997 kcal/mol	184 195@LB@ \| \|@LB@5'-UAU...CCUGA AGCAC...UUA-3'@LB@ UAAAGAGGAA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -11.8586 kcal/mol@LB@Unfolding Energy - mRNA 1.44575 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
189	0.03933	0.6177	b2461	eutP	-9.78	0.045635	227 -- 240	44 -- 56	putative P-loop NTPase ethanolamine utilization protein	_____________226____________241\n_____________\|______________\|\n5'-AAA...GGUAG________C_____AAACA...CCG-3'\n______________CGUCGGGG_AGGAA\n______________\|\|\|\|:::\|_\|\|\|\|\|\n______________GCAGUUUC_UCCUU\n3'-UUU...ACCGG______________AAAGU...ACA-5'\n_____________\|______________\|\n_____________57_____________43\n	228 -- 234	49 -- 55	-15.0697 kcal/mol	4.34178 kcal/mol	0.948902 kcal/mol	226 241@LB@ \| \|@LB@5'-AAA...GGUAG C AAACA...CCG-3'@LB@ CGUCGGGG AGGAA@LB@ \|\|\|\|:::\| \|\|\|\|\|@LB@ GCAGUUUC UCCUU@LB@3'-UUU...ACCGG AAAGU...ACA-5'@LB@ \| \|@LB@ 57 43@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -15.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.34178 kcal/mol@LB@Unfolding Energy - sRNA 0.948902 kcal/mol@LB@@LB@Position - mRNA 227 -- 240@LB@Position - sRNA 44 -- 56@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 49 -- 55@LB@
99	0.01953	0.6177	b2473	ypfH	-12.09	0.015349	8 -- 40	44 -- 76	palmitoyl-CoA esterase activity uncertain physiological substrate	_____________7__________________________________41\n_____________\|__________________________________\|\n____5'-ACUUUCA_____CAAGA_____C___________C______GAGGC...GGG-3'\n______________GGCCG_____UGUUA_UGGUCCGUCAG_G_GGAA\n______________\|\|\|\|:_____:\|:\|\|_\|\|\|:\|\|\|\|\|\|:_\|_\|\|\|\|\n______________CCGGU_____GCGAU_ACCGGGCAGUU_C_CCUU\n___3'-UUUUUUUA_____UAUA______A___________U_U____AAAGU...ACA-5'\n_____________\|__________________________________\|\n_____________77_________________________________43\n	28 -- 34	51 -- 57	-34.8713 kcal/mol	9.35151 kcal/mol	13.433 kcal/mol	7 41@LB@ \| \|@LB@ 5'-ACUUUCA CAAGA C C GAGGC...GGG-3'@LB@ GGCCG UGUUA UGGUCCGUCAG G GGAA@LB@ \|\|\|\|: :\|:\|\| \|\|\|:\|\|\|\|\|\|: \| \|\|\|\|@LB@ CCGGU GCGAU ACCGGGCAGUU C CCUU@LB@ 3'-UUUUUUUA UAUA A U U AAAGU...ACA-5'@LB@ \| \|@LB@ 77 43@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -34.8713 kcal/mol@LB@Unfolding Energy - mRNA 9.35151 kcal/mol@LB@Unfolding Energy - sRNA 13.433 kcal/mol@LB@@LB@Position - mRNA 8 -- 40@LB@Position - sRNA 44 -- 76@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 51 -- 57@LB@
80	0.01709	0.6177	b2498	upp	-4.70	0.418803	173 -- 195	44 -- 70	uracil phosphoribosyltransferase	_____________172_________________________196\n_____________\|___________________________\|\n5'-GGC...UUUUU___G___________C_______A___AGAGU...CCG-3'\n______________UGU_GCU____GCCC_UCAAAGG_GAA\n______________\|:\|_\|\|\|____\|\|\|\|_\|\|\|\|\|\|:_\|\|\|\n______________AUA_CGA____CGGG_AGUUUCU_CUU\n3'-UUU...CGGUU___G___UAAC____C_______C___AAAGU...ACA-5'\n_____________\|___________________________\|\n_____________71__________________________43\n	185 -- 191	48 -- 54	-22.3772 kcal/mol	6.37003 kcal/mol	11.3101 kcal/mol	172 196@LB@ \| \|@LB@5'-GGC...UUUUU G C A AGAGU...CCG-3'@LB@ UGU GCU GCCC UCAAAGG GAA@LB@ \|:\| \|\|\| \|\|\|\| \|\|\|\|\|\|: \|\|\|@LB@ AUA CGA CGGG AGUUUCU CUU@LB@3'-UUU...CGGUU G UAAC C C AAAGU...ACA-5'@LB@ \| \|@LB@ 71 43@LB@@LB@@LB@Energy -4.70 kcal/mol@LB@Hybridization Energy -22.3772 kcal/mol@LB@Unfolding Energy - mRNA 6.37003 kcal/mol@LB@Unfolding Energy - sRNA 11.3101 kcal/mol@LB@@LB@Position - mRNA 173 -- 195@LB@Position - sRNA 44 -- 70@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 48 -- 54@LB@
72	0.015	0.6177	b2513	yfgM	-10.40	0.034106	179 -- 190	45 -- 55	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________178__________191\n_____________\|____________\|\n5'-GGC...ACUGG________A___GAAGG...UUG-3'\n______________GUUAAGGA_GGA\n______________\|\|:\|\|:\|\|_\|\|\|\n______________CAGUUUCU_CCU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	180 -- 186	48 -- 54	-12.2699 kcal/mol	0.940443 kcal/mol	0.930875 kcal/mol	178 191@LB@ \| \|@LB@5'-GGC...ACUGG A GAAGG...UUG-3'@LB@ GUUAAGGA GGA@LB@ \|\|:\|\|:\|\| \|\|\|@LB@ CAGUUUCU CCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -10.40 kcal/mol@LB@Hybridization Energy -12.2699 kcal/mol@LB@Unfolding Energy - mRNA 0.940443 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 179 -- 190@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 48 -- 54@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@
32	0.006131	0.6129	b2585	pssA	-9.74	0.046374	32 -- 41	45 -- 54	phosphatidylserine synthase; CDP-diacylglycerol-serine O-phosphatidyltransferase	_____________31_________42\n_____________\|__________\|\n5'-CGC...CCAGC__________GAUCG...CCG-3'\n______________UCGAAGAGGG\n______________\|\|:\|\|\|\|\|\|:\n______________AGUUUCUCCU\n3'-UUU...CGGGC__________UAAAG...ACA-5'\n_____________\|__________\|\n_____________55_________44\n	35 -- 41	45 -- 51	-13.2862 kcal/mol	2.61225 kcal/mol	0.929144 kcal/mol	31 42@LB@ \| \|@LB@5'-CGC...CCAGC GAUCG...CCG-3'@LB@ UCGAAGAGGG@LB@ \|\|:\|\|\|\|\|\|:@LB@ AGUUUCUCCU@LB@3'-UUU...CGGGC UAAAG...ACA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -13.2862 kcal/mol@LB@Unfolding Energy - mRNA 2.61225 kcal/mol@LB@Unfolding Energy - sRNA 0.929144 kcal/mol@LB@@LB@Position - mRNA 32 -- 41@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 35 -- 41@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

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