Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
9	0.000195	0.07335	b1830	prc	-15.09	0.015143	131 -- 161	7 -- 38	carboxy-terminal protease for penicillin-binding protein 3	_____________130______________________________162\n_____________\|________________________________\|\n5'-CGA...UCCAG___________U___UCUU____U________CAGAA...CGG-3'\n______________CUGAAUUCGGG_AUG____UGAU__GUGCGCG\n______________\|\|\|\|\|\|\|\|:\|\|_\|\|\|____\|:\|:__:\|\|\|\|\|\|\n______________GACUUAAGUCC_UAC____AUUG__UACGCGC\n3'-UUU...GUAGA___________C___UACU____UU_______AGAAAG-5'\n_____________\|________________________________\|\n_____________39_______________________________6\n	155 -- 161	7 -- 13	-31.7028 kcal/mol	7.25259 kcal/mol	9.35859 kcal/mol	130 162@LB@ \| \|@LB@5'-CGA...UCCAG U UCUU U CAGAA...CGG-3'@LB@ CUGAAUUCGGG AUG UGAU GUGCGCG@LB@ \|\|\|\|\|\|\|\|:\|\| \|\|\| \|:\|: :\|\|\|\|\|\|@LB@ GACUUAAGUCC UAC AUUG UACGCGC@LB@3'-UUU...GUAGA C UACU UU AGAAAG-5'@LB@ \| \|@LB@ 39 6@LB@@LB@@LB@Energy -15.09 kcal/mol@LB@Hybridization Energy -31.7028 kcal/mol@LB@Unfolding Energy - mRNA 7.25259 kcal/mol@LB@Unfolding Energy - sRNA 9.35859 kcal/mol@LB@@LB@Position - mRNA 131 -- 161@LB@Position - sRNA 7 -- 38@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 7 -- 13@LB@
13	0.0003435	0.08948	b2551	glyA	-14.51	0.019315	147 -- 213	7 -- 69	serine hydroxymethyltransferase	_____________146____________________________________________________________________214\n_____________\|______________________________________________________________________\|\n5'-CAA...CCAAC___A______UAUAAA_______A________GUUAG___________A____CG____U__________AAAUG...UCG-3'\n______________AGG_CCGC_C______GGCCAAA_AUUUUAUU_____CUGAG_UCAGG_GAUG__GAUG_UAAA_GCGUG\n______________\|\|\|_\|\|:\|_\|______\|\|\|\|\|\|\|_\|\|\|\|:\|\|:_____\|\|\|\|:_\|\|\|\|\|_\|\|\|\|__\|\|\|:_:\|\|\|_\|\|\|:\|\n______________UCC_GGUG_G______CCGGUUU_UAAAGUAG_____GACUU_AGUCC_CUAC__CUAU_GUUU_CGCGC\n________3'-UUU________A_CACUCA________________A_________A__________UA____U____A_____AGAAAG-5'\n_____________\|______________________________________________________________________\|\n_____________70_____________________________________________________________________6\n	162 -- 168	48 -- 54	-52.4461 kcal/mol	16.168 kcal/mol	21.7638 kcal/mol	146 214@LB@ \| \|@LB@5'-CAA...CCAAC A UAUAAA A GUUAG A CG U AAAUG...UCG-3'@LB@ AGG CCGC C GGCCAAA AUUUUAUU CUGAG UCAGG GAUG GAUG UAAA GCGUG@LB@ \|\|\| \|\|:\| \| \|\|\|\|\|\|\| \|\|\|\|:\|\|: \|\|\|\|: \|\|\|\|\| \|\|\|\| \|\|\|: :\|\|\| \|\|\|:\|@LB@ UCC GGUG G CCGGUUU UAAAGUAG GACUU AGUCC CUAC CUAU GUUU CGCGC@LB@ 3'-UUU A CACUCA A A UA U A AGAAAG-5'@LB@ \| \|@LB@ 70 6@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -52.4461 kcal/mol@LB@Unfolding Energy - mRNA 16.168 kcal/mol@LB@Unfolding Energy - sRNA 21.7638 kcal/mol@LB@@LB@Position - mRNA 147 -- 213@LB@Position - sRNA 7 -- 69@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 48 -- 54@LB@
28	0.001743	0.2094	b2308	hisQ	-15.00	0.015715	1 -- 16	7 -- 21	histidine ABC transporter permease	______________1_______________17\n______________\|_______________\|\n___________5'-_________C______AAGCA...UUG-3'\n______________GAUAACGAA_UGCGCG\n______________\|\|\|\|\|\|:\|\|_\|\|\|\|\|\|\n______________CUAUUGUUU_ACGCGC\n3'-UUU...UACUA________________AGAAAG-5'\n_____________\|________________\|\n_____________22_______________6\n	3 -- 9	13 -- 19	-21.0778 kcal/mol	4.83206 kcal/mol	1.24179 kcal/mol	1 17@LB@ \| \|@LB@ 5'- C AAGCA...UUG-3'@LB@ GAUAACGAA UGCGCG@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\|\|@LB@ CUAUUGUUU ACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -15.00 kcal/mol@LB@Hybridization Energy -21.0778 kcal/mol@LB@Unfolding Energy - mRNA 4.83206 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 1 -- 16@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 13 -- 19@LB@
29	0.001844	0.2094	b2047	wcaJ	-13.26	0.032615	200 -- 222	7 -- 21	colanic biosynthesis UDP-glucose lipid carrier transferase	_____________199_____________________223\n_____________\|_______________________\|\n5'-GCA...ACAAC__________CUAAAAAA_____AGCGA...UAU-3'\n______________GAUGACAAAU________GCGCG\n______________\|\|\|:\|\|\|\|\|\|________\|\|\|\|\|\n______________CUAUUGUUUA________CGCGC\n3'-UUU...UACUA_______________________AGAAAG-5'\n_____________\|_______________________\|\n_____________22______________________6\n	203 -- 209	12 -- 18	-17.5174 kcal/mol	3.01646 kcal/mol	1.24179 kcal/mol	199 223@LB@ \| \|@LB@5'-GCA...ACAAC CUAAAAAA AGCGA...UAU-3'@LB@ GAUGACAAAU GCGCG@LB@ \|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUUUA CGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -17.5174 kcal/mol@LB@Unfolding Energy - mRNA 3.01646 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 200 -- 222@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 12 -- 18@LB@
31	0.001974	0.2094	b1080	flgI	-10.59	0.096403	87 -- 101	7 -- 21	putative flagellar basal body protein	_____________86______________102\n_____________\|_______________\|\n5'-AUU...ACUCA_______________CAUUG...AAA-3'\n______________GGUGGCGGAUGCGCG\n______________\|:\|::\|::\|\|\|\|\|\|\|\n______________CUAUUGUUUACGCGC\n3'-UUU...UACUA_______________AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	95 -- 101	7 -- 13	-22.6939 kcal/mol	10.8668 kcal/mol	1.24179 kcal/mol	86 102@LB@ \| \|@LB@5'-AUU...ACUCA CAUUG...AAA-3'@LB@ GGUGGCGGAUGCGCG@LB@ \|:\|::\|::\|\|\|\|\|\|\|@LB@ CUAUUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -22.6939 kcal/mol@LB@Unfolding Energy - mRNA 10.8668 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 87 -- 101@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 7 -- 13@LB@
32	0.001981	0.2094	b3110	yhaO	-10.61	0.095420	268 -- 283	7 -- 23	putative transporter	_____________267_______________284\n_____________\|_________________\|\n5'-AAU...AAUGA____G____________AGAAG...UCG-3'\n______________GUGA_AGCGAGUG_GCG\n______________:\|\|\|_\|:\|:\|:\|\|_\|\|\|\n______________UACU_UUGUUUAC_CGC\n3'-UUU...CCUAC____A________G___AGAAAG-5'\n_____________\|_________________\|\n_____________24________________6\n	274 -- 280	11 -- 17	-15.5882 kcal/mol	2.45682 kcal/mol	2.52012 kcal/mol	267 284@LB@ \| \|@LB@5'-AAU...AAUGA G AGAAG...UCG-3'@LB@ GUGA AGCGAGUG GCG@LB@ :\|\|\| \|:\|:\|:\|\| \|\|\|@LB@ UACU UUGUUUAC CGC@LB@3'-UUU...CCUAC A G AGAAAG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -15.5882 kcal/mol@LB@Unfolding Energy - mRNA 2.45682 kcal/mol@LB@Unfolding Energy - sRNA 2.52012 kcal/mol@LB@@LB@Position - mRNA 268 -- 283@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 11 -- 17@LB@
36	0.002407	0.2206	b2550	yphH	-13.17	0.033778	238 -- 251	7 -- 20	putative DNA-binding transcriptional regulator	_____________237____________252\n_____________\|______________\|\n5'-AGG...CCACC______________AUUCU...UGG-3'\n______________AUAACAAAUGCGUG\n______________\|\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UAUUGUUUACGCGC\n3'-UUU...ACUAC______________AGAAAG-5'\n_____________\|______________\|\n_____________21_____________6\n	245 -- 251	7 -- 13	-19.0929 kcal/mol	4.67933 kcal/mol	1.23906 kcal/mol	237 252@LB@ \| \|@LB@5'-AGG...CCACC AUUCU...UGG-3'@LB@ AUAACAAAUGCGUG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UAUUGUUUACGCGC@LB@3'-UUU...ACUAC AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -19.0929 kcal/mol@LB@Unfolding Energy - mRNA 4.67933 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 238 -- 251@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 7 -- 13@LB@
43	0.003009	0.2325	b3429	glgA	-8.59	0.206361	152 -- 163	7 -- 22	glycogen synthase	_____________151______________164\n_____________\|________________\|\n5'-GUA...CGUGC________________AAAUG...ACG-3'\n______________UGGUAAC____GCGCG\n______________\|\|:\|\|\|\|____\|\|\|\|\|\n______________ACUAUUG____CGCGC\n3'-UUU...CUACU_______UUUA_____AGAAAG-5'\n_____________\|________________\|\n_____________23_______________6\n	152 -- 158	16 -- 22	-13.429 kcal/mol	3.59934 kcal/mol	1.24379 kcal/mol	151 164@LB@ \| \|@LB@5'-GUA...CGUGC AAAUG...ACG-3'@LB@ UGGUAAC GCGCG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ ACUAUUG CGCGC@LB@3'-UUU...CUACU UUUA AGAAAG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -8.59 kcal/mol@LB@Hybridization Energy -13.429 kcal/mol@LB@Unfolding Energy - mRNA 3.59934 kcal/mol@LB@Unfolding Energy - sRNA 1.24379 kcal/mol@LB@@LB@Position - mRNA 152 -- 163@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 16 -- 22@LB@
46	0.003408	0.2484	b2518	ndk	-12.77	0.039848	1 -- 16	7 -- 21	multifunctional nucleoside diphosphate kinase and apyrimidinic endonuclease and 3'-phosphodiesterase	______________1_______________17\n______________\|_______________\|\n___________5'-___________A____GGGCA...AAA-3'\n______________GGUGAUGGAUG_CGUG\n______________\|:\|:\|:::\|\|\|_\|\|:\|\n______________CUAUUGUUUAC_GCGC\n3'-UUU...UACUA________________AGAAAG-5'\n_____________\|________________\|\n_____________22_______________6\n	5 -- 11	11 -- 17	-16.3595 kcal/mol	2.34366 kcal/mol	1.24179 kcal/mol	1 17@LB@ \| \|@LB@ 5'- A GGGCA...AAA-3'@LB@ GGUGAUGGAUG CGUG@LB@ \|:\|:\|:::\|\|\| \|\|:\|@LB@ CUAUUGUUUAC GCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -16.3595 kcal/mol@LB@Unfolding Energy - mRNA 2.34366 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 1 -- 16@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 11 -- 17@LB@
53	0.004896	0.3024	b3790	wecD	-9.15	0.167607	125 -- 139	7 -- 21	TDP-fucosamine acetyltransferase	_____________124_____________140\n_____________\|_______________\|\n5'-CUG...GGCUC_________G_____AAGCG...UGA-3'\n______________GAUGACGAG_GUGUG\n______________\|\|\|:\|\|:\|:_\|:\|:\|\n______________CUAUUGUUU_CGCGC\n3'-UUU...UACUA_________A_____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	126 -- 132	14 -- 20	-15.9636 kcal/mol	5.57309 kcal/mol	1.24179 kcal/mol	124 140@LB@ \| \|@LB@5'-CUG...GGCUC G AAGCG...UGA-3'@LB@ GAUGACGAG GUGUG@LB@ \|\|\|:\|\|:\|: \|:\|:\|@LB@ CUAUUGUUU CGCGC@LB@3'-UUU...UACUA A AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -15.9636 kcal/mol@LB@Unfolding Energy - mRNA 5.57309 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 125 -- 139@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 14 -- 20@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)

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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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