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
14	0.003078	0.593	b0886	cydC	-10.90	0.026971	183 -- 199	39 -- 56	glutathione/cysteine ABC transporter export permease/ATPase	_____________182________________200\n_____________\|__________________\|\n5'-GCG...CCCAU_____________A____AAUGC...UCG-3'\n______________CGUC_AGGAGGAG_UUUA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|:\|\n______________GCAG_UUCUCCUU_AAGU\n3'-UUU...ACCGG____U________A____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	188 -- 194	44 -- 50	-16.2318 kcal/mol	4.17801 kcal/mol	1.15786 kcal/mol	182 200@LB@ \| \|@LB@5'-GCG...CCCAU A AAUGC...UCG-3'@LB@ CGUC AGGAGGAG UUUA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|:\|@LB@ GCAG UUCUCCUU AAGU@LB@3'-UUU...ACCGG U A AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -16.2318 kcal/mol@LB@Unfolding Energy - mRNA 4.17801 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 183 -- 199@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
15	0.003313	0.593	b3133	agaV	-12.53	0.012445	185 -- 194	44 -- 53	N-acetylgalactosamine-specific enzyme IIB component of PTS	_____________184________195\n_____________\|__________\|\n5'-UCA...CAAAA__________CACGC...UAG-3'\n______________CAAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	188 -- 194	44 -- 50	-14.1596 kcal/mol	0.702602 kcal/mol	0.927997 kcal/mol	184 195@LB@ \| \|@LB@5'-UCA...CAAAA CACGC...UAG-3'@LB@ CAAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -14.1596 kcal/mol@LB@Unfolding Energy - mRNA 0.702602 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@
16	0.003381	0.593	b0956	matP	-12.11	0.015217	269 -- 280	42 -- 53	Ter macrodomain organizer matS-binding protein	_____________268__________281\n_____________\|____________\|\n5'-UUU...CAUCG____________AAUCA...AAG-3'\n______________CGAAGGGGAGUU\n______________\|:\|\|\|:\|\|\|:\|\|\n______________GUUUCUCCUUAA\n3'-UUU...GGGCA____________AGUAA...ACA-5'\n_____________\|____________\|\n_____________54___________41\n	274 -- 280	42 -- 48	-15.3716 kcal/mol	2.33274 kcal/mol	0.933904 kcal/mol	268 281@LB@ \| \|@LB@5'-UUU...CAUCG AAUCA...AAG-3'@LB@ CGAAGGGGAGUU@LB@ \|:\|\|\|:\|\|\|:\|\|@LB@ GUUUCUCCUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -15.3716 kcal/mol@LB@Unfolding Energy - mRNA 2.33274 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 269 -- 280@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 42 -- 48@LB@
17	0.003407	0.593	b3607	cysE	-9.56	0.050591	4 -- 44	27 -- 56	serine acetyltransferase	_____________3__________________________________________45\n_____________\|__________________________________________\|\n________5'-CGG_______AUGCCAAUAACC______A_____CAAG_______AUUGC...CGA-3'\n______________CGUUGAA____________GAGGAA_UUUAU_____UAUUAU\n______________\|\|\|::\|\|____________\|\|\|\|\|\|_\|\|:\|\|_____\|\|\|\|\|\|\n______________GCAGUUU____________CUCCUU_AAGUA_____AUAAUA\n3'-UUU...ACCGG_________________________A_____AAAAA______AUACG...ACA-5'\n_____________\|__________________________________________\|\n_____________57_________________________________________26\n	4 -- 10	50 -- 56	-14.2001 kcal/mol	3.44433 kcal/mol	1.19682 kcal/mol	3 45@LB@ \| \|@LB@ 5'-CGG AUGCCAAUAACC A CAAG AUUGC...CGA-3'@LB@ CGUUGAA GAGGAA UUUAU UAUUAU@LB@ \|\|\|::\|\| \|\|\|\|\|\| \|\|:\|\| \|\|\|\|\|\|@LB@ GCAGUUU CUCCUU AAGUA AUAAUA@LB@3'-UUU...ACCGG A AAAAA AUACG...ACA-5'@LB@ \| \|@LB@ 57 26@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -14.2001 kcal/mol@LB@Unfolding Energy - mRNA 3.44433 kcal/mol@LB@Unfolding Energy - sRNA 1.19682 kcal/mol@LB@@LB@Position - mRNA 4 -- 44@LB@Position - sRNA 27 -- 56@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 50 -- 56@LB@
18	0.003456	0.593	b0867	amiD	-11.23	0.023022	276 -- 289	39 -- 52	1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein	_____________275____________290\n_____________\|______________\|\n5'-GAU...UCGAG__________A___GCUUG...CCC-3'\n______________AAAGAGGGAU_UCA\n______________\|\|\|\|\|\|\|:\|\|_\|\|\|\n______________UUUCUCCUUA_AGU\n3'-UUU...GGCAG__________A___AAAAA...ACA-5'\n_____________\|______________\|\n_____________53_____________38\n	279 -- 285	43 -- 49	-14.4178 kcal/mol	2.13665 kcal/mol	1.05043 kcal/mol	275 290@LB@ \| \|@LB@5'-GAU...UCGAG A GCUUG...CCC-3'@LB@ AAAGAGGGAU UCA@LB@ \|\|\|\|\|\|\|:\|\| \|\|\|@LB@ UUUCUCCUUA AGU@LB@3'-UUU...GGCAG A AAAAA...ACA-5'@LB@ \| \|@LB@ 53 38@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -14.4178 kcal/mol@LB@Unfolding Energy - mRNA 2.13665 kcal/mol@LB@Unfolding Energy - sRNA 1.05043 kcal/mol@LB@@LB@Position - mRNA 276 -- 289@LB@Position - sRNA 39 -- 52@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 43 -- 49@LB@
19	0.003501	0.593	b2019	hisG	-12.73	0.011332	183 -- 194	43 -- 54	ATP phosphoribosyltransferase	_____________182__________195\n_____________\|____________\|\n5'-UUU...CAGGU____________AACAA...AUC-3'\n______________UUAAAGAGGAAU\n______________\|:\|\|\|\|\|\|\|\|\|\|\n______________AGUUUCUCCUUA\n3'-UUU...CGGGC____________AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	188 -- 194	43 -- 49	-14.9017 kcal/mol	1.23041 kcal/mol	0.944705 kcal/mol	182 195@LB@ \| \|@LB@5'-UUU...CAGGU AACAA...AUC-3'@LB@ UUAAAGAGGAAU@LB@ \|:\|\|\|\|\|\|\|\|\|\|@LB@ AGUUUCUCCUUA@LB@3'-UUU...CGGGC AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -14.9017 kcal/mol@LB@Unfolding Energy - mRNA 1.23041 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
20	0.00399	0.5992	b4175	hflC	-10.54	0.031960	184 -- 196	43 -- 56	HflB protease modulator specific for phage lambda cII repressor	_____________183____________197\n_____________\|______________\|\n5'-UUA...ACCAG______________AACGA...GUU-3'\n______________CGUCAGGG_GGAAU\n______________\|\|\|\|\|::\|_\|\|\|\|\|\n______________GCAGUUUC_CCUUA\n3'-UUU...ACCGG________U_____AAGUA...ACA-5'\n_____________\|______________\|\n_____________57_____________42\n	185 -- 191	49 -- 55	-15.8123 kcal/mol	4.32193 kcal/mol	0.953958 kcal/mol	183 197@LB@ \| \|@LB@5'-UUA...ACCAG AACGA...GUU-3'@LB@ CGUCAGGG GGAAU@LB@ \|\|\|\|\|::\| \|\|\|\|\|@LB@ GCAGUUUC CCUUA@LB@3'-UUU...ACCGG U AAGUA...ACA-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -10.54 kcal/mol@LB@Hybridization Energy -15.8123 kcal/mol@LB@Unfolding Energy - mRNA 4.32193 kcal/mol@LB@Unfolding Energy - sRNA 0.953958 kcal/mol@LB@@LB@Position - mRNA 184 -- 196@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 49 -- 55@LB@
21	0.004054	0.5992	b2076	mdtC	-11.67	0.018717	158 -- 193	45 -- 78	multidrug efflux system subunit C	_____________157____________________________________194\n_____________\|______________________________________\|\n5'-CUC...GCAUU____A____AAGC____UU__________UG_______GGCGU...CGG-3'\n______________GUGG_CCAA____CGCU____GCCCGUCA__AAGAGGA\n______________:\|\|\|_\|\|\|\|____\|\|\|\|____\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UACC_GGUU____GCGA____CGGGCAGU__UUCUCCU\n_____3'-UUUUUU_________AUA_____UAAC_________________UAAAG...ACA-5'\n_____________\|______________________________________\|\n_____________79_____________________________________44\n	187 -- 193	45 -- 51	-37.8051 kcal/mol	12.6053 kcal/mol	13.5316 kcal/mol	157 194@LB@ \| \|@LB@5'-CUC...GCAUU A AAGC UU UG GGCGU...CGG-3'@LB@ GUGG CCAA CGCU GCCCGUCA AAGAGGA@LB@ :\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UACC GGUU GCGA CGGGCAGU UUCUCCU@LB@ 3'-UUUUUU AUA UAAC UAAAG...ACA-5'@LB@ \| \|@LB@ 79 44@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -37.8051 kcal/mol@LB@Unfolding Energy - mRNA 12.6053 kcal/mol@LB@Unfolding Energy - sRNA 13.5316 kcal/mol@LB@@LB@Position - mRNA 158 -- 193@LB@Position - sRNA 45 -- 78@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
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@
23	0.004411	0.5992	b3390	aroK	-10.22	0.037117	283 -- 298	39 -- 54	shikimate kinase I	_____________282______________299\n_____________\|________________\|\n5'-UGG...ACAAC____UAU_________CG-3'\n______________UCAA___GGAAUUUUA\n______________\|\|\|\|___\|\|\|\|\|\|\|:\|\n______________AGUU___CCUUAAAGU\n3'-UUU...CGGGC____UCU_________AAAAA...ACA-5'\n_____________\|________________\|\n_____________55_______________38\n	292 -- 298	39 -- 45	-11.8677 kcal/mol	0.499768 kcal/mol	1.1491 kcal/mol	282 299@LB@ \| \|@LB@5'-UGG...ACAAC UAU CG-3'@LB@ UCAA GGAAUUUUA@LB@ \|\|\|\| \|\|\|\|\|\|\|:\|@LB@ AGUU CCUUAAAGU@LB@3'-UUU...CGGGC UCU AAAAA...ACA-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -11.8677 kcal/mol@LB@Unfolding Energy - mRNA 0.499768 kcal/mol@LB@Unfolding Energy - sRNA 1.1491 kcal/mol@LB@@LB@Position - mRNA 283 -- 298@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 39 -- 45@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