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	Additional homologs
19	0.0006629	0.1181	b2909	ygfB	-11.13	0.077732	186 -- 206	4 -- 22	UPF0149 family protein		_____________185___________________207\n_____________\|_____________________\|\n5'-AAA...CCCUU___C_________UUA_____AUACA...UCA-3'\n______________UGA_GACGAAUGC___UGUCU\n______________\|\|\|_:\|\|:\|\|\|\|\|___:\|\|\|\|\n______________ACU_UUGUUUACG___GCAGA\n3'-UUU...CUACU___A_________C_______AAG-5'\n_____________\|_____________________\|\n_____________23____________________3\n	192 -- 198	10 -- 16	-17.2827 kcal/mol	4.89762 kcal/mol	1.2572 kcal/mol	185 207@LB@ \| \|@LB@5'-AAA...CCCUU C UUA AUACA...UCA-3'@LB@ UGA GACGAAUGC UGUCU@LB@ \|\|\| :\|\|:\|\|\|\|\| :\|\|\|\|@LB@ ACU UUGUUUACG GCAGA@LB@3'-UUU...CUACU A C AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -17.2827 kcal/mol@LB@Unfolding Energy - mRNA 4.89762 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 186 -- 206@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 10 -- 16@LB@
198	0.0193	0.3104	b2961	mutY	-10.33	0.106403	22 -- 38	1 -- 15	adenine DNA glycosylase		_____________21________________39\n_____________\|_________________\|\n5'-CGU...CGGUG_____A__U________AUAAA...UAU-3'\n______________AAAUG_CG_CGUUUUUC\n______________\|\|\|\|\|_\|\|_\|\|\|:\|\|\|\|\n______________UUUAC_GC_GCAGAAAG\n3'-UUU...UAUUG_________________-5'\n_____________\|________________\|\n_____________16_______________1\n	32 -- 38	1 -- 7	-14.8981 kcal/mol	3.3462 kcal/mol	1.21803 kcal/mol	21 39@LB@ \| \|@LB@5'-CGU...CGGUG A U AUAAA...UAU-3'@LB@ AAAUG CG CGUUUUUC@LB@ \|\|\|\|\| \|\| \|\|\|:\|\|\|\|@LB@ UUUAC GC GCAGAAAG@LB@3'-UUU...UAUUG -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -14.8981 kcal/mol@LB@Unfolding Energy - mRNA 3.3462 kcal/mol@LB@Unfolding Energy - sRNA 1.21803 kcal/mol@LB@@LB@Position - mRNA 22 -- 38@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 1 -- 7@LB@
127	0.01249	0.3104	b2964	nupG	-12.57	0.043346	150 -- 164	1 -- 16	nucleoside transporter	b2406	_____________149______________165\n_____________\|________________\|\n5'-UCC...ACGGU________________AAACA...UGA-3'\n______________CAAAUGUGC_UUUUUC\n______________\|\|\|\|\|\|:\|\|_\|:\|\|\|\|\n______________GUUUACGCG_AGAAAG\n3'-UUU...CUAUU_________C______-5'\n_____________\|_______________\|\n_____________17______________1\n	152 -- 158	8 -- 14	-16.6758 kcal/mol	2.8679 kcal/mol	1.23857 kcal/mol	149 165@LB@ \| \|@LB@5'-UCC...ACGGU AAACA...UGA-3'@LB@ CAAAUGUGC UUUUUC@LB@ \|\|\|\|\|\|:\|\| \|:\|\|\|\|@LB@ GUUUACGCG AGAAAG@LB@3'-UUU...CUAUU C -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -16.6758 kcal/mol@LB@Unfolding Energy - mRNA 2.8679 kcal/mol@LB@Unfolding Energy - sRNA 1.23857 kcal/mol@LB@@LB@Position - mRNA 150 -- 164@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 8 -- 14@LB@
129	0.01261	0.3104	b3025	qseB	-10.92	0.084347	141 -- 152	5 -- 17	quorum sensing DNA-binding response regulator in two-component regulatory system with QseC		_____________140___________153\n_____________\|_____________\|\n5'-GUG...GCUGU_____________ACAAC...GUC-3'\n______________ACAGA_GCGCGUU\n______________\|\|\|:\|_\|\|\|\|\|\|:\n______________UGUUU_CGCGCAG\n3'-UUU...ACUAU_____A_______AAAG-5'\n_____________\|_____________\|\n_____________18____________4\n	146 -- 152	5 -- 11	-15.7823 kcal/mol	3.63703 kcal/mol	1.22241 kcal/mol	140 153@LB@ \| \|@LB@5'-GUG...GCUGU ACAAC...GUC-3'@LB@ ACAGA GCGCGUU@LB@ \|\|\|:\| \|\|\|\|\|\|:@LB@ UGUUU CGCGCAG@LB@3'-UUU...ACUAU A AAAG-5'@LB@ \| \|@LB@ 18 4@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -15.7823 kcal/mol@LB@Unfolding Energy - mRNA 3.63703 kcal/mol@LB@Unfolding Energy - sRNA 1.22241 kcal/mol@LB@@LB@Position - mRNA 141 -- 152@LB@Position - sRNA 5 -- 17@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 5 -- 11@LB@
56	0.005155	0.3024	b3091	uxaA	-13.05	0.035558	147 -- 159	6 -- 19	altronate hydrolase		_____________146____________160\n_____________\|______________\|\n5'-CUG...UGCUU______________GACUA...CGC-3'\n______________UAAC_AAUGCGCGU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AUUG_UUACGCGCA\n3'-UUU...CUACU____U_________GAAAG-5'\n_____________\|______________\|\n_____________20_____________5\n	153 -- 159	6 -- 12	-17.3524 kcal/mol	3.0727 kcal/mol	1.22941 kcal/mol	146 160@LB@ \| \|@LB@5'-CUG...UGCUU GACUA...CGC-3'@LB@ UAAC AAUGCGCGU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ AUUG UUACGCGCA@LB@3'-UUU...CUACU U GAAAG-5'@LB@ \| \|@LB@ 20 5@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -17.3524 kcal/mol@LB@Unfolding Energy - mRNA 3.0727 kcal/mol@LB@Unfolding Energy - sRNA 1.22941 kcal/mol@LB@@LB@Position - mRNA 147 -- 159@LB@Position - sRNA 6 -- 19@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 6 -- 12@LB@
57	0.005155	0.3024	b3091	uxaA	-13.05	0.035558	147 -- 159	6 -- 19	altronate hydrolase		_____________146____________160\n_____________\|______________\|\n5'-CUG...UGCUU______________GACUA...CGC-3'\n______________UAAC_AAUGCGCGU\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AUUG_UUACGCGCA\n3'-UUU...CUACU____U_________GAAAG-5'\n_____________\|______________\|\n_____________20_____________5\n	153 -- 159	6 -- 12	-17.3524 kcal/mol	3.0727 kcal/mol	1.22941 kcal/mol	146 160@LB@ \| \|@LB@5'-CUG...UGCUU GACUA...CGC-3'@LB@ UAAC AAUGCGCGU@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ AUUG UUACGCGCA@LB@3'-UUU...CUACU U GAAAG-5'@LB@ \| \|@LB@ 20 5@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -17.3524 kcal/mol@LB@Unfolding Energy - mRNA 3.0727 kcal/mol@LB@Unfolding Energy - sRNA 1.22941 kcal/mol@LB@@LB@Position - mRNA 147 -- 159@LB@Position - sRNA 6 -- 19@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 6 -- 12@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@
185	0.01831	0.3104	b3164	pnp	-7.42	0.310961	131 -- 137	8 -- 14	polynucleotide phosphorylase/polyadenylase		_____________130_____138\n_____________\|_______\|\n5'-AGC...GCGAG_______AGAAG...UUA-3'\n______________GAUGCGC\n______________:\|\|\|\|\|\|\n______________UUACGCG\n3'-UUU...AUUGU_______CAGAAAG-5'\n_____________\|_______\|\n_____________15______7\n	131 -- 137	8 -- 14	-10.1419 kcal/mol	2.24272 kcal/mol	0.481462 kcal/mol	130 138@LB@ \| \|@LB@5'-AGC...GCGAG AGAAG...UUA-3'@LB@ GAUGCGC@LB@ :\|\|\|\|\|\|@LB@ UUACGCG@LB@3'-UUU...AUUGU CAGAAAG-5'@LB@ \| \|@LB@ 15 7@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -10.1419 kcal/mol@LB@Unfolding Energy - mRNA 2.24272 kcal/mol@LB@Unfolding Energy - sRNA 0.481462 kcal/mol@LB@@LB@Position - mRNA 131 -- 137@LB@Position - sRNA 8 -- 14@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 8 -- 14@LB@
100	0.01004	0.3104	b3166	truB	-9.42	0.151044	113 -- 128	5 -- 18	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase		_____________112______________129\n_____________\|________________\|\n5'-GGC...GGUUG__G________AU___AAACC...AAC-3'\n______________AA_GGAUGCGC__GUC\n______________\|\|_::\|\|\|\|\|\|__\|\|\|\n______________UU_UUUACGCG__CAG\n3'-UUU...UACUA__G_____________AAAG-5'\n_____________\|________________\|\n_____________19_______________4\n	117 -- 123	8 -- 14	-15.4757 kcal/mol	4.82661 kcal/mol	1.2243 kcal/mol	112 129@LB@ \| \|@LB@5'-GGC...GGUUG G AU AAACC...AAC-3'@LB@ AA GGAUGCGC GUC@LB@ \|\| ::\|\|\|\|\|\| \|\|\|@LB@ UU UUUACGCG CAG@LB@3'-UUU...UACUA G AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -15.4757 kcal/mol@LB@Unfolding Energy - mRNA 4.82661 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 113 -- 128@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 8 -- 14@LB@
132	0.01286	0.3104	b3176	glmM	-8.35	0.224806	246 -- 258	8 -- 20	phosphoglucosamine mutase		_____________245___________259\n_____________\|_____________\|\n5'-GUU...GUCGU____G________CGAUC...CGG-3'\n______________GUAG_GGAUGCGC\n______________:\|\|:_::\|\|\|\|\|\|\n______________UAUU_UUUACGCG\n3'-UUU...ACUAC____G________CAGAAAG-5'\n_____________\|_____________\|\n_____________21____________7\n	252 -- 258	8 -- 14	-14.3134 kcal/mol	4.73041 kcal/mol	1.23367 kcal/mol	245 259@LB@ \| \|@LB@5'-GUU...GUCGU G CGAUC...CGG-3'@LB@ GUAG GGAUGCGC@LB@ :\|\|: ::\|\|\|\|\|\|@LB@ UAUU UUUACGCG@LB@3'-UUU...ACUAC G CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -8.35 kcal/mol@LB@Hybridization Energy -14.3134 kcal/mol@LB@Unfolding Energy - mRNA 4.73041 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 8 -- 14@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

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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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