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
128	0.01258	0.3104	b0677	nagA	-7.18	0.336330	272 -- 297	1 -- 22	N-acetylglucosamine-6-phosphate deacetylase		_____________271________________________298\n_____________\|__________________________\|\n5'-AAC...AUCGC_______CU___UAAAA______G__CGG-3'\n______________UGAUGGC__GAU_____GCGUCU_UC\n______________\|\|\|\|::\|__:\|\|_____\|\|\|\|\|\|_\|\|\n______________ACUAUUG__UUA_____CGCAGA_AG\n3'-UUU...CUACU_______U____CG_________A__-5'\n_____________\|_________________________\|\n_____________23________________________1\n	272 -- 278	16 -- 22	-15.3811 kcal/mol	6.93964 kcal/mol	1.25963 kcal/mol	271 298@LB@ \| \|@LB@5'-AAC...AUCGC CU UAAAA G CGG-3'@LB@ UGAUGGC GAU GCGUCU UC@LB@ \|\|\|\|::\| :\|\| \|\|\|\|\|\| \|\|@LB@ ACUAUUG UUA CGCAGA AG@LB@3'-UUU...CUACU U CG A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -15.3811 kcal/mol@LB@Unfolding Energy - mRNA 6.93964 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 272 -- 297@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 16 -- 22@LB@
172	0.01719	0.3104	b0678	nagB	-13.42	0.030481	5 -- 26	1 -- 17	glucosamine-6-phosphate deaminase		_____________4______________________27\n_____________\|______________________\|\n_______5'-UAUC______UAAAC___________GUGAG...GUC-3'\n______________GCAAAU_____GCGUGUCUUUU\n______________:\|\|\|\|\|_____\|\|\|:\|\|\|\|\|\|:\n______________UGUUUA_____CGCGCAGAAAG\n3'-UUU...ACUAU______________________-5'\n_____________\|_____________________\|\n_____________18____________________1\n	20 -- 26	1 -- 7	-18.2092 kcal/mol	3.54695 kcal/mol	1.23994 kcal/mol	4 27@LB@ \| \|@LB@ 5'-UAUC UAAAC GUGAG...GUC-3'@LB@ GCAAAU GCGUGUCUUUU@LB@ :\|\|\|\|\| \|\|\|:\|\|\|\|\|\|:@LB@ UGUUUA CGCGCAGAAAG@LB@3'-UUU...ACUAU -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -18.2092 kcal/mol@LB@Unfolding Energy - mRNA 3.54695 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 5 -- 26@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 20 -- 26@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@
115	0.01182	0.3104	b3367	nirC	-10.39	0.104055	218 -- 233	4 -- 19	nitrite transporter		_____________217______________234\n_____________\|________________\|\n5'-AUG...ACUAU_____________G__AACGC...UGG-3'\n______________UAAUAAGUGUGCG_CU\n______________\|\|\|:\|\|:\|\|:\|\|\|_\|\|\n______________AUUGUUUACGCGC_GA\n3'-UUU...CUACU_____________A__AAG-5'\n_____________\|________________\|\n_____________20_______________3\n	224 -- 230	7 -- 13	-17.3607 kcal/mol	5.72929 kcal/mol	1.2406 kcal/mol	217 234@LB@ \| \|@LB@5'-AUG...ACUAU G AACGC...UGG-3'@LB@ UAAUAAGUGUGCG CU@LB@ \|\|\|:\|\|:\|\|:\|\|\| \|\|@LB@ AUUGUUUACGCGC GA@LB@3'-UUU...CUACU A AAG-5'@LB@ \| \|@LB@ 20 3@LB@@LB@@LB@Energy -10.39 kcal/mol@LB@Hybridization Energy -17.3607 kcal/mol@LB@Unfolding Energy - mRNA 5.72929 kcal/mol@LB@Unfolding Energy - sRNA 1.2406 kcal/mol@LB@@LB@Position - mRNA 218 -- 233@LB@Position - sRNA 4 -- 19@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 7 -- 13@LB@
134	0.01294	0.3104	b2234	nrdA	-13.57	0.028625	217 -- 231	7 -- 22	ribonucleoside-diphosphate reductase 1 alpha subunit		_____________216______________232\n_____________\|________________\|\n5'-GAC...UCUGC________________ACGGU...UGC-3'\n______________UGGUGACAAA_GCGCG\n______________\|\|:\|:\|\|\|\|\|_\|\|\|\|\|\n______________ACUAUUGUUU_CGCGC\n3'-UUU...CUACU__________A_____AGAAAG-5'\n_____________\|________________\|\n_____________23_______________6\n	220 -- 226	13 -- 19	-19.6051 kcal/mol	4.78775 kcal/mol	1.24379 kcal/mol	216 232@LB@ \| \|@LB@5'-GAC...UCUGC ACGGU...UGC-3'@LB@ UGGUGACAAA GCGCG@LB@ \|\|:\|:\|\|\|\|\| \|\|\|\|\|@LB@ ACUAUUGUUU CGCGC@LB@3'-UUU...CUACU A AGAAAG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -19.6051 kcal/mol@LB@Unfolding Energy - mRNA 4.78775 kcal/mol@LB@Unfolding Energy - sRNA 1.24379 kcal/mol@LB@@LB@Position - mRNA 217 -- 231@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 13 -- 19@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@
200	0.0195	0.3104	b3183	obgE	-7.01	0.355777	76 -- 83	4 -- 11	GTPase involved in cell partioning and DNA repair		_____________75_______84\n_____________\|________\|\n5'-UUU...UCUCG________GUCGU...GCC-3'\n______________GUGCGUUU\n______________\|:\|\|\|\|:\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	77 -- 83	4 -- 10	-11.428 kcal/mol	3.26207 kcal/mol	1.15639 kcal/mol	75 84@LB@ \| \|@LB@5'-UUU...UCUCG GUCGU...GCC-3'@LB@ GUGCGUUU@LB@ \|:\|\|\|\|:\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.01 kcal/mol@LB@Hybridization Energy -11.428 kcal/mol@LB@Unfolding Energy - mRNA 3.26207 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 4 -- 10@LB@
16	0.0004819	0.102	b0957	ompA	-13.00	0.036257	182 -- 195	8 -- 22	outer membrane protein A (3a;II*;G;d)		_____________181_____________196\n_____________\|_______________\|\n5'-CUU...UUGGA_______________AAAAA...AAC-3'\n______________UGAUAACGAG_GCGC\n______________\|\|\|\|\|\|\|:\|:_\|\|\|\|\n______________ACUAUUGUUU_CGCG\n3'-UUU...CUACU__________A____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	185 -- 191	13 -- 19	-17.7455 kcal/mol	3.5039 kcal/mol	1.23838 kcal/mol	181 196@LB@ \| \|@LB@5'-CUU...UUGGA AAAAA...AAC-3'@LB@ UGAUAACGAG GCGC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\|@LB@ ACUAUUGUUU CGCG@LB@3'-UUU...CUACU A CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -13.00 kcal/mol@LB@Hybridization Energy -17.7455 kcal/mol@LB@Unfolding Energy - mRNA 3.5039 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 182 -- 195@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 13 -- 19@LB@
99	0.009943	0.3104	b3405	ompR	-10.46	0.101388	231 -- 245	8 -- 21	response regulator in two-component regulatory system with EnvZ		_____________230_____________246\n_____________\|_______________\|\n5'-AAU...UGGUC________C______CUGCG...GCG-3'\n______________GAUGACGA_AUGCGC\n______________\|\|\|:\|\|:\|_\|\|\|\|\|\|\n______________CUAUUGUU_UACGCG\n3'-UUU...UACUA_______________CAGAAAG-5'\n_____________\|_______________\|\n_____________22______________7\n	232 -- 238	14 -- 20	-17.2341 kcal/mol	5.5408 kcal/mol	1.23638 kcal/mol	230 246@LB@ \| \|@LB@5'-AAU...UGGUC C CUGCG...GCG-3'@LB@ GAUGACGA AUGCGC@LB@ \|\|\|:\|\|:\| \|\|\|\|\|\|@LB@ CUAUUGUU UACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -17.2341 kcal/mol@LB@Unfolding Energy - mRNA 5.5408 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 231 -- 245@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 14 -- 20@LB@
8	0.000167	0.07068	b0814	ompX	-11.11	0.078421	202 -- 223	1 -- 22	outer membrane protein X		_____________201____________________224\n_____________\|______________________\|\n5'-CUG...GGUUA___AAAA__U___A________AGCAC...CAC-3'\n______________UGA____AA_UGC_UGUCUUUC\n______________\|\|\|____\|\|_\|\|\|_:\|\|\|\|\|\|\|\n______________ACU____UU_ACG_GCAGAAAG\n3'-UUU...CUACU___AUUG__U___C________-5'\n_____________\|_____________________\|\n_____________23____________________1\n	217 -- 223	1 -- 7	-15.5509 kcal/mol	3.18554 kcal/mol	1.25963 kcal/mol	201 224@LB@ \| \|@LB@5'-CUG...GGUUA AAAA U A AGCAC...CAC-3'@LB@ UGA AA UGC UGUCUUUC@LB@ \|\|\| \|\| \|\|\| :\|\|\|\|\|\|\|@LB@ ACU UU ACG GCAGAAAG@LB@3'-UUU...CUACU AUUG U C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -15.5509 kcal/mol@LB@Unfolding Energy - mRNA 3.18554 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 202 -- 223@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 1 -- 7@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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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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