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
175	0.01743	0.3104	b0921	smtA	-12.81	0.039244	146 -- 164	2 -- 20	putative S-adenosyl-L-methionine-dependent methyltransferase		_____________145_________________165\n_____________\|___________________\|\n5'-AUC...UGGCU________AUA________AUCAG...AUC-3'\n______________GUGACAAA___GCGUCUUU\n______________:\|:\|\|\|\|\|___\|\|\|\|\|\|\|\|\n______________UAUUGUUU___CGCAGAAA\n3'-UUU...ACUAC________ACG________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	158 -- 164	2 -- 8	-18.7664 kcal/mol	4.69909 kcal/mol	1.25604 kcal/mol	145 165@LB@ \| \|@LB@5'-AUC...UGGCU AUA AUCAG...AUC-3'@LB@ GUGACAAA GCGUCUUU@LB@ :\|:\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UAUUGUUU CGCAGAAA@LB@3'-UUU...ACUAC ACG G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -12.81 kcal/mol@LB@Hybridization Energy -18.7664 kcal/mol@LB@Unfolding Energy - mRNA 4.69909 kcal/mol@LB@Unfolding Energy - sRNA 1.25604 kcal/mol@LB@@LB@Position - mRNA 146 -- 164@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 2 -- 8@LB@
52	0.004683	0.3024	b1130	phoP	-12.79	0.039529	186 -- 208	6 -- 31	response regulator in two-component regulatory system with PhoQ		_____________185________________________209\n_____________\|__________________________\|\n5'-GAG...UAAGA_________A________________ACUGG...CCA-3'\n______________CAGGGA_GA__AUAA_AAAUGCGCGU\n______________\|\|\|\|\|\|_\|\|__\|\|\|\|_\|\|\|\|\|\|\|\|\|\|\n______________GUCCCU_CU__UAUU_UUUACGCGCA\n3'-UUU...CUUAA______A__AC____G__________GAAAG-5'\n_____________\|__________________________\|\n_____________32_________________________5\n	202 -- 208	6 -- 12	-26.853 kcal/mol	6.30535 kcal/mol	7.75407 kcal/mol	185 209@LB@ \| \|@LB@5'-GAG...UAAGA A ACUGG...CCA-3'@LB@ CAGGGA GA AUAA AAAUGCGCGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ GUCCCU CU UAUU UUUACGCGCA@LB@3'-UUU...CUUAA A AC G GAAAG-5'@LB@ \| \|@LB@ 32 5@LB@@LB@@LB@Energy -12.79 kcal/mol@LB@Hybridization Energy -26.853 kcal/mol@LB@Unfolding Energy - mRNA 6.30535 kcal/mol@LB@Unfolding Energy - sRNA 7.75407 kcal/mol@LB@@LB@Position - mRNA 186 -- 208@LB@Position - sRNA 6 -- 31@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 6 -- 12@LB@
73	0.006809	0.3087	b4146	epmB	-12.79	0.039583	278 -- 298	1 -- 22	EF-P-Lys34 lysylation protein; weak lysine 2 3-aminomutase		_____________277____________________299\n_____________\|______________________\|\n5'-UUC...GAUCC______ACUUC___________GA-3'\n______________UGAUGA______UGCGUCUUUU\n______________\|\|\|\|:\|______:\|\|\|\|\|\|\|\|:\n______________ACUAUU______GCGCAGAAAG\n3'-UUU...CUACU______GUUUAC__________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	292 -- 298	1 -- 7	-16.8007 kcal/mol	2.75078 kcal/mol	1.25963 kcal/mol	277 299@LB@ \| \|@LB@5'-UUC...GAUCC ACUUC GA-3'@LB@ UGAUGA UGCGUCUUUU@LB@ \|\|\|\|:\| :\|\|\|\|\|\|\|\|:@LB@ ACUAUU GCGCAGAAAG@LB@3'-UUU...CUACU GUUUAC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.79 kcal/mol@LB@Hybridization Energy -16.8007 kcal/mol@LB@Unfolding Energy - mRNA 2.75078 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 278 -- 298@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@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@
96	0.009671	0.3104	b0941	elfG	-12.70	0.041082	222 -- 232	5 -- 15	putative fimbrial-like adhesin protein	b3145 b0533	_____________221_________233\n_____________\|___________\|\n5'-UUU...GAGAA___________AUUAC...GGC-3'\n______________AAAUGCGUGUC\n______________\|\|\|\|\|\|\|:\|\|\|\n______________UUUACGCGCAG\n3'-UUU...UAUUG___________AAAG-5'\n_____________\|___________\|\n_____________16__________4\n	226 -- 232	5 -- 11	-17.0283 kcal/mol	3.13128 kcal/mol	1.19708 kcal/mol	221 233@LB@ \| \|@LB@5'-UUU...GAGAA AUUAC...GGC-3'@LB@ AAAUGCGUGUC@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ UUUACGCGCAG@LB@3'-UUU...UAUUG AAAG-5'@LB@ \| \|@LB@ 16 4@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -17.0283 kcal/mol@LB@Unfolding Energy - mRNA 3.13128 kcal/mol@LB@Unfolding Energy - sRNA 1.19708 kcal/mol@LB@@LB@Position - mRNA 222 -- 232@LB@Position - sRNA 5 -- 15@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 5 -- 11@LB@
78	0.007118	0.3087	b1118	lolE	-12.65	0.041861	19 -- 36	6 -- 21	lipoprotein-releasing system transmembrane protein		_____________18_________________37\n_____________\|__________________\|\n5'-CUG...CUACC______CUC_________AACGC...GCA-3'\n______________GGUAAC___GAUGCGCGU\n______________\|:\|\|\|\|___:\|\|\|\|\|\|\|\|\n______________CUAUUG___UUACGCGCA\n3'-UUU...UACUA______U___________GAAAG-5'\n_____________\|__________________\|\n_____________22_________________5\n	30 -- 36	6 -- 12	-20.2716 kcal/mol	6.37224 kcal/mol	1.24519 kcal/mol	18 37@LB@ \| \|@LB@5'-CUG...CUACC CUC AACGC...GCA-3'@LB@ GGUAAC GAUGCGCGU@LB@ \|:\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ CUAUUG UUACGCGCA@LB@3'-UUU...UACUA U GAAAG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -12.65 kcal/mol@LB@Hybridization Energy -20.2716 kcal/mol@LB@Unfolding Energy - mRNA 6.37224 kcal/mol@LB@Unfolding Energy - sRNA 1.24519 kcal/mol@LB@@LB@Position - mRNA 19 -- 36@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 6 -- 12@LB@
71	0.006638	0.3087	b3857	mobA	-12.61	0.042607	253 -- 264	7 -- 18	molybdopterin-guanine dinucleotide synthase		_____________252__________265\n_____________\|____________\|\n5'-UCC...AGCCA________G___GCGUA...AAC-3'\n______________GACGAAUG_GCG\n______________:\|\|:\|\|\|\|_\|\|\|\n______________UUGUUUAC_CGC\n3'-UUU...UACUA________G___AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	254 -- 260	11 -- 17	-15.9619 kcal/mol	2.14186 kcal/mol	1.20891 kcal/mol	252 265@LB@ \| \|@LB@5'-UCC...AGCCA G GCGUA...AAC-3'@LB@ GACGAAUG GCG@LB@ :\|\|:\|\|\|\| \|\|\|@LB@ UUGUUUAC CGC@LB@3'-UUU...UACUA G AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -12.61 kcal/mol@LB@Hybridization Energy -15.9619 kcal/mol@LB@Unfolding Energy - mRNA 2.14186 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 253 -- 264@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 11 -- 17@LB@
121	0.01226	0.3104	b3209	elbB	-12.57	0.043302	225 -- 240	4 -- 18	isoprenoid biosynthesis protein with amidotransferase-like domain		_____________224______________241\n_____________\|________________\|\n5'-GCG...UUCUG__________G_____AUGAC...GUG-3'\n______________AGCGGAUGCG_CGUCU\n______________\|:\|::\|\|\|\|\|_\|\|\|\|\|\n______________UUGUUUACGC_GCAGA\n3'-UUU...UACUA________________AAG-5'\n_____________\|________________\|\n_____________19_______________3\n	228 -- 234	9 -- 15	-20.315 kcal/mol	6.5132 kcal/mol	1.22995 kcal/mol	224 241@LB@ \| \|@LB@5'-GCG...UUCUG G AUGAC...GUG-3'@LB@ AGCGGAUGCG CGUCU@LB@ \|:\|::\|\|\|\|\| \|\|\|\|\|@LB@ UUGUUUACGC GCAGA@LB@3'-UUU...UACUA AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -20.315 kcal/mol@LB@Unfolding Energy - mRNA 6.5132 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 225 -- 240@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 9 -- 15@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@
30	0.001906	0.2094	b0616	citE	-12.56	0.043465	103 -- 116	8 -- 21	citrate lyase citryl-ACP lyase (beta) subunit		_____________102____________117\n_____________\|______________\|\n5'-CAA...AUGUC_________G____ACUGG...UCU-3'\n______________GAUGACAAA_GCGC\n______________\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CUAUUGUUU_CGCG\n3'-UUU...UACUA_________A____CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	105 -- 111	13 -- 19	-17.9482 kcal/mol	4.14919 kcal/mol	1.23638 kcal/mol	102 117@LB@ \| \|@LB@5'-CAA...AUGUC G ACUGG...UCU-3'@LB@ GAUGACAAA GCGC@LB@ \|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CUAUUGUUU CGCG@LB@3'-UUU...UACUA A CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -12.56 kcal/mol@LB@Hybridization Energy -17.9482 kcal/mol@LB@Unfolding Energy - mRNA 4.14919 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 103 -- 116@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 13 -- 19@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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usability assessment

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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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