Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
114	0.007692	0.2368	b0584	fepA	-13.71	0.055244	241 -- 265	1 -- 26	ferrienterobactin outer membrane transporter	_____________240________________________266\n_____________\|__________________________\|\n5'-GAA...CAAUC___________U____U____CA___ACAAG...ACG-3'\n______________UGGGGAU_UUA_GGGG_AGCG__GGC\n______________\|\|\|\|\|\|:_\|:\|_:\|::_\|\|\|:__\|\|\|\n______________ACCCCUG_AGU_UCUU_UCGU__CCG\n3'-UUU...GUUUU_______U___U____U____CA___-5'\n_____________\|_________________________\|\n_____________27________________________1\n	241 -- 247	20 -- 26	-24.8633 kcal/mol	8.63835 kcal/mol	2.51842 kcal/mol	240 266@LB@ \| \|@LB@5'-GAA...CAAUC U U CA ACAAG...ACG-3'@LB@ UGGGGAU UUA GGGG AGCG GGC@LB@ \|\|\|\|\|\|: \|:\| :\|:: \|\|\|: \|\|\|@LB@ ACCCCUG AGU UCUU UCGU CCG@LB@3'-UUU...GUUUU U U U CA -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -13.71 kcal/mol@LB@Hybridization Energy -24.8633 kcal/mol@LB@Unfolding Energy - mRNA 8.63835 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 241 -- 265@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 20 -- 26@LB@
44	0.002166	0.1648	b3349	slyD	-19.18	0.001707	20 -- 41	5 -- 23	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)	_____________19_____________________42\n_____________\|______________________\|\n5'-UGU...AGUGC__________UGC_________ACAAA...ACU-3'\n______________GGACAUCAGA___GAGAAGCAG\n______________\|\|\|\|\|\|\|\|:\|___\|\|:\|\|\|\|\|\|\n______________CCUGUAGUUU___CUUUUCGUC\n3'-UUU...UUACC______________________ACCG-5'\n_____________\|______________________\|\n_____________24_____________________4\n	35 -- 41	5 -- 11	-25.7728 kcal/mol	5.01574 kcal/mol	1.57523 kcal/mol	19 42@LB@ \| \|@LB@5'-UGU...AGUGC UGC ACAAA...ACU-3'@LB@ GGACAUCAGA GAGAAGCAG@LB@ \|\|\|\|\|\|\|\|:\| \|\|:\|\|\|\|\|\|@LB@ CCUGUAGUUU CUUUUCGUC@LB@3'-UUU...UUACC ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -19.18 kcal/mol@LB@Hybridization Energy -25.7728 kcal/mol@LB@Unfolding Energy - mRNA 5.01574 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 20 -- 41@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 5 -- 11@LB@
113	0.00768	0.2368	b1923	fliC	-14.29	0.040892	38 -- 54	4 -- 25	flagellar filament structural protein (flagellin)	_____________37_____________________55\n_____________\|______________________\|\n5'-GUU...AAUAA______________________AUUUC...CUU-3'\n______________GGGG____CAGAGAAAAG_AGU\n______________\|\|\|\|____\|\|:\|\|\|\|\|\|\|_\|\|\|\n______________CCCC____GUUUCUUUUC_UCA\n3'-UUU...UUUUA____UGUA__________G___CCG-5'\n_____________\|______________________\|\n_____________26_____________________3\n	45 -- 51	8 -- 14	-19.9416 kcal/mol	3.14092 kcal/mol	2.51306 kcal/mol	37 55@LB@ \| \|@LB@5'-GUU...AAUAA AUUUC...CUU-3'@LB@ GGGG CAGAGAAAAG AGU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CCCC GUUUCUUUUC UCA@LB@3'-UUU...UUUUA UGUA G CCG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -14.29 kcal/mol@LB@Hybridization Energy -19.9416 kcal/mol@LB@Unfolding Energy - mRNA 3.14092 kcal/mol@LB@Unfolding Energy - sRNA 2.51306 kcal/mol@LB@@LB@Position - mRNA 38 -- 54@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 8 -- 14@LB@
184	0.0132	0.2504	b2897	sdhE	-10.91	0.194803	203 -- 220	7 -- 23	flavinator of succinate dehydrogenase; antitoxin of CptAB toxin-antitoxin pair	_____________202________________221\n_____________\|__________________\|\n5'-GUA...AAGAU_________CAAC_____CCGCA...ACA-3'\n______________GGACAUUAA____AAAGC\n______________\|\|\|\|\|\|:\|\|____\|\|\|\|\|\n______________CCUGUAGUU____UUUCG\n3'-UUU...UUACC_________UCU______UCACCG-5'\n_____________\|__________________\|\n_____________24_________________6\n	205 -- 211	15 -- 21	-14.6885 kcal/mol	3.17611 kcal/mol	0.599063 kcal/mol	202 221@LB@ \| \|@LB@5'-GUA...AAGAU CAAC CCGCA...ACA-3'@LB@ GGACAUUAA AAAGC@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\|@LB@ CCUGUAGUU UUUCG@LB@3'-UUU...UUACC UCU UCACCG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -14.6885 kcal/mol@LB@Unfolding Energy - mRNA 3.17611 kcal/mol@LB@Unfolding Energy - sRNA 0.599063 kcal/mol@LB@@LB@Position - mRNA 203 -- 220@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 15 -- 21@LB@
151	0.01116	0.2504	b0903	pflB	-10.70	0.211701	140 -- 166	4 -- 34	formate C-acetyltransferase 1 anaerobic; pyruvate formate-lyase 1	_____________139_____________________________167\n_____________\|_______________________________\|\n5'-CAC...GACCA____U______U__________UAC______AAAUA...ACU-3'\n______________CCAU__AAUGG___UGUCGAAG____GCAGU\n______________\|\|\|:__\|\|\|\|\|___::\|\|:\|\|\|____\|\|\|\|\|\n______________GGUG__UUACC___GUAGUUUC____CGUCA\n3'-UUU...CCCGA____UU_____CCU________UUUU_____CCG-5'\n_____________\|_______________________________\|\n_____________35______________________________3\n	152 -- 158	13 -- 19	-21.5315 kcal/mol	6.56187 kcal/mol	4.26884 kcal/mol	139 167@LB@ \| \|@LB@5'-CAC...GACCA U U UAC AAAUA...ACU-3'@LB@ CCAU AAUGG UGUCGAAG GCAGU@LB@ \|\|\|: \|\|\|\|\| ::\|\|:\|\|\| \|\|\|\|\|@LB@ GGUG UUACC GUAGUUUC CGUCA@LB@3'-UUU...CCCGA UU CCU UUUU CCG-5'@LB@ \| \|@LB@ 35 3@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -21.5315 kcal/mol@LB@Unfolding Energy - mRNA 6.56187 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 140 -- 166@LB@Position - sRNA 4 -- 34@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 13 -- 19@LB@
147	0.01091	0.2504	b2720	hycF	-14.84	0.030299	116 -- 133	1 -- 16	formate hydrogenlyase complex iron-sulfur protein	_____________115________________134\n_____________\|__________________\|\n5'-CGA...CGUAA___________AA_____GCCGU...CAG-3'\n______________GAAGAAGAGCA__GUGGU\n______________:\|\|\|\|\|:\|\|\|\|__\|\|\|\|:\n______________UUUCUUUUCGU__CACCG\n3'-UUU...UGUAG__________________-5'\n_____________\|_________________\|\n_____________17________________1\n	120 -- 126	6 -- 12	-19.8629 kcal/mol	3.67538 kcal/mol	1.34555 kcal/mol	115 134@LB@ \| \|@LB@5'-CGA...CGUAA AA GCCGU...CAG-3'@LB@ GAAGAAGAGCA GUGGU@LB@ :\|\|\|\|\|:\|\|\|\| \|\|\|\|:@LB@ UUUCUUUUCGU CACCG@LB@3'-UUU...UGUAG -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -19.8629 kcal/mol@LB@Unfolding Energy - mRNA 3.67538 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 116 -- 133@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 6 -- 12@LB@
108	0.007234	0.2348	b1725	yniA	-14.77	0.031588	182 -- 211	1 -- 32	fructosamine kinase family protein	_____________181_________________________________212\n_____________\|___________________________________\|\n5'-GAG...GGCAG____C_____AGA_______UGU____________AAUCA...GGC-3'\n______________ACAA_AUGGG___GACAUCA______GGCA__GGC\n______________\|\|\|\|_\|\|\|\|\|___\|\|\|\|\|\|\|______:\|\|\|__\|\|\|\n______________UGUU_UACCC___CUGUAGU______UCGU__CCG\n3'-UUU...CGAGG____U_______________UUCUUU____CA___-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	195 -- 201	16 -- 22	-26.2676 kcal/mol	8.96188 kcal/mol	2.53929 kcal/mol	181 212@LB@ \| \|@LB@5'-GAG...GGCAG C AGA UGU AAUCA...GGC-3'@LB@ ACAA AUGGG GACAUCA GGCA GGC@LB@ \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| :\|\|\| \|\|\|@LB@ UGUU UACCC CUGUAGU UCGU CCG@LB@3'-UUU...CGAGG U UUCUUU CA -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.77 kcal/mol@LB@Hybridization Energy -26.2676 kcal/mol@LB@Unfolding Energy - mRNA 8.96188 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 182 -- 211@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 16 -- 22@LB@
155	0.01136	0.2504	b2168	fruK	-7.75	0.545043	91 -- 105	7 -- 22	fructose-1-phosphate kinase	_____________90_______________106\n_____________\|________________\|\n5'-AAA...CACUU________________CAUCG...CCA-3'\n______________GGCGUU_AAGAAAGGU\n______________\|:\|:\|:_\|\|\|\|\|\|:\|:\n______________CUGUAG_UUCUUUUCG\n3'-UUU...UACCC______U_________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	99 -- 105	7 -- 13	-14.0922 kcal/mol	5.75103 kcal/mol	0.590875 kcal/mol	90 106@LB@ \| \|@LB@5'-AAA...CACUU CAUCG...CCA-3'@LB@ GGCGUU AAGAAAGGU@LB@ \|:\|:\|: \|\|\|\|\|\|:\|:@LB@ CUGUAG UUCUUUUCG@LB@3'-UUU...UACCC U UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -7.75 kcal/mol@LB@Hybridization Energy -14.0922 kcal/mol@LB@Unfolding Energy - mRNA 5.75103 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 91 -- 105@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 7 -- 13@LB@
56	0.002838	0.1778	b3371	frlB	-17.11	0.007704	196 -- 228	2 -- 32	fructoselysine-6-P-deglycase	_____________195________________________________229\n_____________\|__________________________________\|\n5'-ACU...AGAAA________UU_________U________CC____ACUUU...ACG-3'\n______________AUAAAAUG__GGAUAUUGA__AAAAGCA__GUGG\n______________\|:\|\|\|\|\|\|__\|\|\|:\|\|::\|__\|\|\|\|\|\|\|__\|\|\|\|\n______________UGUUUUAC__CCUGUAGUU__UUUUCGU__CACC\n3'-UUU...CGAGG________C__________UC_____________G-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	216 -- 222	6 -- 12	-25.2618 kcal/mol	5.61622 kcal/mol	2.53929 kcal/mol	195 229@LB@ \| \|@LB@5'-ACU...AGAAA UU U CC ACUUU...ACG-3'@LB@ AUAAAAUG GGAUAUUGA AAAAGCA GUGG@LB@ \|:\|\|\|\|\|\| \|\|\|:\|\|::\| \|\|\|\|\|\|\| \|\|\|\|@LB@ UGUUUUAC CCUGUAGUU UUUUCGU CACC@LB@3'-UUU...CGAGG C UC G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -17.11 kcal/mol@LB@Hybridization Energy -25.2618 kcal/mol@LB@Unfolding Energy - mRNA 5.61622 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 196 -- 228@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 6 -- 12@LB@
77	0.004622	0.2062	b1241	adhE	-12.78	0.086641	182 -- 205	1 -- 21	fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase	_____________181______________________206\n_____________\|________________________\|\n5'-AAU...GUUUA______UC_________UUA____UGUUA...AAA-3'\n______________ACAUUA__AGGAGAGCA___UGGC\n______________\|\|\|\|:\|__\|\|:\|:\|\|\|\|___\|\|\|\|\n______________UGUAGU__UCUUUUCGU___ACCG\n3'-UUU...ACCCC______U__________C______-5'\n_____________\|_______________________\|\n_____________22______________________1\n	192 -- 198	6 -- 12	-20.8292 kcal/mol	6.5343 kcal/mol	1.51103 kcal/mol	181 206@LB@ \| \|@LB@5'-AAU...GUUUA UC UUA UGUUA...AAA-3'@LB@ ACAUUA AGGAGAGCA UGGC@LB@ \|\|\|\|:\| \|\|:\|:\|\|\|\| \|\|\|\|@LB@ UGUAGU UCUUUUCGU ACCG@LB@3'-UUU...ACCCC U C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -20.8292 kcal/mol@LB@Unfolding Energy - mRNA 6.5343 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 182 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 6 -- 12@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