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	Additional homologs
106	0.007048	0.2333	b4512	ybdD	-9.12	0.369799	33 -- 54	1 -- 25	DUF466 family protein	b4353	_____________32________________________55\n_____________\|_________________________\|\n5'-GCA...GAGGG___________C___U_________UUAGU...GGG-3'\n______________GGGGAUGUUGG_GAA__GU__UGGC\n______________\|\|\|\|\|::\|:::_\|\|\|__\|:__\|\|\|\|\n______________CCCCUGUAGUU_CUU__CG__ACCG\n3'-UUU...UUUUA___________U___UU__UC____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	36 -- 42	16 -- 22	-21.5624 kcal/mol	9.92515 kcal/mol	2.51748 kcal/mol	32 55@LB@ \| \|@LB@5'-GCA...GAGGG C U UUAGU...GGG-3'@LB@ GGGGAUGUUGG GAA GU UGGC@LB@ \|\|\|\|\|::\|::: \|\|\| \|: \|\|\|\|@LB@ CCCCUGUAGUU CUU CG ACCG@LB@3'-UUU...UUUUA U UU UC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -21.5624 kcal/mol@LB@Unfolding Energy - mRNA 9.92515 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 33 -- 54@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 16 -- 22@LB@
107	0.007146	0.2343	b0085	murE	-14.50	0.036427	193 -- 205	1 -- 25	UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso- diaminopimelate ligase		_____________192_______________________206\n_____________\|_________________________\|\n5'-UGC...GGCGA_________________________AGAUC...CGG-3'\n______________GGGGACA____________GGUGGC\n______________\|\|\|\|\|\|\|____________:\|\|\|\|\|\n______________CCCCUGU____________UCACCG\n3'-UUU...UUUUA_______AGUUUCUUUUCG______-5'\n_____________\|________________________\|\n_____________26_______________________1\n	193 -- 199	19 -- 25	-21.3886 kcal/mol	4.36682 kcal/mol	2.51748 kcal/mol	192 206@LB@ \| \|@LB@5'-UGC...GGCGA AGAUC...CGG-3'@LB@ GGGGACA GGUGGC@LB@ \|\|\|\|\|\|\| :\|\|\|\|\|@LB@ CCCCUGU UCACCG@LB@3'-UUU...UUUUA AGUUUCUUUUCG -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -21.3886 kcal/mol@LB@Unfolding Energy - mRNA 4.36682 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 19 -- 25@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@
111	0.007434	0.2348	b0103	coaE	-19.66	0.001155	224 -- 242	1 -- 25	dephospho-CoA kinase		_____________223________________________243\n_____________\|__________________________\|\n5'-UAU...UUAAC___A______________________AAGAG...AUA-3'\n______________GGG_GGCAUU_______GGCAGUGGC\n______________\|\|\|_\|:\|\|\|:_______:\|\|\|\|\|\|\|\|\n______________CCC_CUGUAG_______UCGUCACCG\n3'-UUU...UUUUA__________UUUCUUU_________-5'\n_____________\|_________________________\|\n_____________26________________________1\n	236 -- 242	1 -- 7	-28.3462 kcal/mol	6.16994 kcal/mol	2.51748 kcal/mol	223 243@LB@ \| \|@LB@5'-UAU...UUAAC A AAGAG...AUA-3'@LB@ GGG GGCAUU GGCAGUGGC@LB@ \|\|\| \|:\|\|\|: :\|\|\|\|\|\|\|\|@LB@ CCC CUGUAG UCGUCACCG@LB@3'-UUU...UUUUA UUUCUUU -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -19.66 kcal/mol@LB@Hybridization Energy -28.3462 kcal/mol@LB@Unfolding Energy - mRNA 6.16994 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 224 -- 242@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 1 -- 7@LB@
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@
115	0.007886	0.2401	b2890	lysS	-11.64	0.144658	161 -- 186	1 -- 20	lysine tRNA synthetase constitutive	b4129	_____________160_________________________187\n_____________\|___________________________\|\n5'-AAA...CAAUU________CAAGUUU____________UAUGA...GGA-3'\n______________UAUCGAAG_______GAAAGCAG_GGU\n______________:\|\|\|:\|\|\|_______:\|\|\|\|\|\|\|_\|\|:\n______________GUAGUUUC_______UUUUCGUC_CCG\n3'-UUU...CCCCU_______________________A___-5'\n_____________\|__________________________\|\n_____________21_________________________1\n	177 -- 183	5 -- 11	-18.6981 kcal/mol	5.60124 kcal/mol	1.45855 kcal/mol	160 187@LB@ \| \|@LB@5'-AAA...CAAUU CAAGUUU UAUGA...GGA-3'@LB@ UAUCGAAG GAAAGCAG GGU@LB@ :\|\|\|:\|\|\| :\|\|\|\|\|\|\| \|\|:@LB@ GUAGUUUC UUUUCGUC CCG@LB@3'-UUU...CCCCU A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -18.6981 kcal/mol@LB@Unfolding Energy - mRNA 5.60124 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 161 -- 186@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 5 -- 11@LB@
117	0.008014	0.2404	b3052	hldE	-12.77	0.087254	132 -- 161	1 -- 30	heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase		_____________131______________________________162\n_____________\|________________________________\|\n5'-GCG...UGGCA_______CUG___G_____AU___________AUUAU...CGC-3'\n______________GAAGUGG____GU_GAAGA__GAAGUA_UGGU\n______________:\|\|:\|\|\|____:\|_:\|\|\|\|__:\|\|\|:\|_\|\|\|:\n______________UUUUACC____UA_UUUCU__UUUCGU_ACCG\n3'-UUU...AGGUG_______CCUG__G_____________C____-5'\n_____________\|_______________________________\|\n_____________31______________________________1\n	132 -- 138	24 -- 30	-21.0542 kcal/mol	5.76621 kcal/mol	2.51911 kcal/mol	131 162@LB@ \| \|@LB@5'-GCG...UGGCA CUG G AU AUUAU...CGC-3'@LB@ GAAGUGG GU GAAGA GAAGUA UGGU@LB@ :\|\|:\|\|\| :\| :\|\|\|\| :\|\|\|:\| \|\|\|:@LB@ UUUUACC UA UUUCU UUUCGU ACCG@LB@3'-UUU...AGGUG CCUG G C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -21.0542 kcal/mol@LB@Unfolding Energy - mRNA 5.76621 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 132 -- 161@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 24 -- 30@LB@
121	0.008566	0.2484	b3466	yhhL	-13.33	0.066537	119 -- 150	1 -- 32	DUF1145 family protein		_____________118_________________________________151\n_____________\|___________________________________\|\n5'-GUU...UUCCA_____C___UCAUU_____________________GGGUC...UUA-3'\n______________GCAAA_UGG_____ACAUC_GGGAAAA__AGUGGC\n______________:\|\|\|\|_\|\|\|_____\|\|\|\|\|_::\|\|\|\|\|__\|\|\|\|\|\|\n______________UGUUU_ACC_____UGUAG_UUCUUUU__UCACCG\n3'-UUU...CGAGG_____U___CC________U_______CG______-5'\n_____________\|__________________________________\|\n_____________33_________________________________1\n	138 -- 144	9 -- 15	-23.4834 kcal/mol	7.61069 kcal/mol	2.53929 kcal/mol	118 151@LB@ \| \|@LB@5'-GUU...UUCCA C UCAUU GGGUC...UUA-3'@LB@ GCAAA UGG ACAUC GGGAAAA AGUGGC@LB@ :\|\|\|\| \|\|\| \|\|\|\|\| ::\|\|\|\|\| \|\|\|\|\|\|@LB@ UGUUU ACC UGUAG UUCUUUU UCACCG@LB@3'-UUU...CGAGG U CC U CG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -13.33 kcal/mol@LB@Hybridization Energy -23.4834 kcal/mol@LB@Unfolding Energy - mRNA 7.61069 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 119 -- 150@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 9 -- 15@LB@
123	0.008923	0.2491	b3243	aaeR	-15.21	0.024673	72 -- 99	1 -- 34	transcriptional regulator for aaeXAB operon		_____________71_________________________________100\n_____________\|__________________________________\|\n5'-AAC...UGUCG________AA__________________C_____GAGAG...UCA-3'\n______________CCGCAGAG___GGGCAU____GGAAAGC_G_GGC\n______________\|\|:\|\|:\|:___\|\|:\|\|\|____\|:\|\|\|\|\|_\|_\|\|\|\n______________GGUGUUUU___CCUGUA____CUUUUCG_C_CCG\n3'-UUU...CCCGA________ACC______GUUU_______U_A___-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	88 -- 94	7 -- 13	-28.4227 kcal/mol	8.94529 kcal/mol	4.26884 kcal/mol	71 100@LB@ \| \|@LB@5'-AAC...UGUCG AA C GAGAG...UCA-3'@LB@ CCGCAGAG GGGCAU GGAAAGC G GGC@LB@ \|\|:\|\|:\|: \|\|:\|\|\| \|:\|\|\|\|\| \| \|\|\|@LB@ GGUGUUUU CCUGUA CUUUUCG C CCG@LB@3'-UUU...CCCGA ACC GUUU U A -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -28.4227 kcal/mol@LB@Unfolding Energy - mRNA 8.94529 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 72 -- 99@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 7 -- 13@LB@
126	0.009112	0.2491	b0299	insF1	-12.99	0.078544	136 -- 158	1 -- 32	IS3 transposase B	b0372 b0541 b1026 b2089 b3558	_____________135______________________________159\n_____________\|________________________________\|\n5'-ACU...AGCUG______C_________________________UAUCC...GUC-3'\n______________GCAGAA__GGGAU______GAAGAGC__UGGC\n______________:\|\|:\|\|__\|\|\|\|:______\|\|\|:\|\|\|__\|\|\|\|\n______________UGUUUU__CCCUG______CUUUUCG__ACCG\n3'-UUU...CGAGG______AC_____UAGUUU_______UC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	148 -- 154	7 -- 13	-22.7833 kcal/mol	7.25293 kcal/mol	2.53929 kcal/mol	135 159@LB@ \| \|@LB@5'-ACU...AGCUG C UAUCC...GUC-3'@LB@ GCAGAA GGGAU GAAGAGC UGGC@LB@ :\|\|:\|\| \|\|\|\|: \|\|\|:\|\|\| \|\|\|\|@LB@ UGUUUU CCCUG CUUUUCG ACCG@LB@3'-UUU...CGAGG AC UAGUUU UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.99 kcal/mol@LB@Hybridization Energy -22.7833 kcal/mol@LB@Unfolding Energy - mRNA 7.25293 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 136 -- 158@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 7 -- 13@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:

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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

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