Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
33	0.006009	0.5385	b1264	trpE	-12.63	0.036478	39 -- 48	79 -- 88	component I of anthranilate synthase	_____________38_________49\n_____________\|__________\|\n5'-UGU...UACGC__________AAAAA...CGG-3'\n______________AAGUUCACGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________UUCAAGUGCA\n3'-CGC...GCGUU__________ACCGA...AAG-5'\n_____________\|__________\|\n_____________89_________78\n	42 -- 48	79 -- 85	-13.8612 kcal/mol	0.721964 kcal/mol	0.505265 kcal/mol	38 49@LB@ \| \|@LB@5'-UGU...UACGC AAAAA...CGG-3'@LB@ AAGUUCACGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UUCAAGUGCA@LB@3'-CGC...GCGUU ACCGA...AAG-5'@LB@ \| \|@LB@ 89 78@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -13.8612 kcal/mol@LB@Unfolding Energy - mRNA 0.721964 kcal/mol@LB@Unfolding Energy - sRNA 0.505265 kcal/mol@LB@@LB@Position - mRNA 39 -- 48@LB@Position - sRNA 79 -- 88@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 79 -- 85@LB@
42	0.008798	0.5385	b0087	mraY	-9.88	0.111048	142 -- 153	79 -- 90	phospho-N-acetylmuramoyl-pentapeptide transferase	_____________141__________154\n_____________\|____________\|\n5'-GAC...UAGUU____________AGUGC...CGC-3'\n______________AAGGGUUCACGU\n______________\|\|::\|\|\|\|\|\|\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	147 -- 153	79 -- 85	-14.1224 kcal/mol	3.73912 kcal/mol	0.506924 kcal/mol	141 154@LB@ \| \|@LB@5'-GAC...UAGUU AGUGC...CGC-3'@LB@ AAGGGUUCACGU@LB@ \|\|::\|\|\|\|\|\|\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -14.1224 kcal/mol@LB@Unfolding Energy - mRNA 3.73912 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 79 -- 85@LB@
103	0.01739	0.5385	b0945	pyrD	-8.62	0.180746	193 -- 204	79 -- 90	dihydro-orotate oxidase FMN-linked	_____________192__________205\n_____________\|____________\|\n5'-UGU...UCCAG____________ACUAC...CGU-3'\n______________GAGAGUUCAUGU\n______________:\|:\|\|\|\|\|\|:\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	198 -- 204	79 -- 85	-13.8118 kcal/mol	4.6828 kcal/mol	0.506924 kcal/mol	192 205@LB@ \| \|@LB@5'-UGU...UCCAG ACUAC...CGU-3'@LB@ GAGAGUUCAUGU@LB@ :\|:\|\|\|\|\|\|:\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -13.8118 kcal/mol@LB@Unfolding Energy - mRNA 4.6828 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 193 -- 204@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 79 -- 85@LB@
134	0.0229	0.5385	b3729	glmS	-8.05	0.223933	255 -- 266	79 -- 90	L-glutamine:D-fructose-6-phosphate aminotransferase	_____________254__________267\n_____________\|____________\|\n5'-CAG...UUCUU____________CGUCU...GUC-3'\n______________GAAGGUUUACGU\n______________:\|\|:\|\|\|:\|\|\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	260 -- 266	79 -- 85	-12.2414 kcal/mol	3.68327 kcal/mol	0.506924 kcal/mol	254 267@LB@ \| \|@LB@5'-CAG...UUCUU CGUCU...GUC-3'@LB@ GAAGGUUUACGU@LB@ :\|\|:\|\|\|:\|\|\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -12.2414 kcal/mol@LB@Unfolding Energy - mRNA 3.68327 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 255 -- 266@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 79 -- 85@LB@
71	0.01305	0.5385	b3843	ubiD	-10.23	0.096580	123 -- 132	80 -- 89	3-octaprenyl-4-hydroxybenzoate decarboxylase	_____________122________133\n_____________\|__________\|\n5'-CGC...CCGUC__________CUAAU...UGG-3'\n______________AGAGUUCACG\n______________\|:\|\|\|\|\|\|\|\|\n______________UUUCAAGUGC\n3'-CGC...GGCGU__________AACCG...AAG-5'\n_____________\|__________\|\n_____________90_________79\n	126 -- 132	80 -- 86	-13.04 kcal/mol	2.30553 kcal/mol	0.506316 kcal/mol	122 133@LB@ \| \|@LB@5'-CGC...CCGUC CUAAU...UGG-3'@LB@ AGAGUUCACG@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUUCAAGUGC@LB@3'-CGC...GGCGU AACCG...AAG-5'@LB@ \| \|@LB@ 90 79@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -13.04 kcal/mol@LB@Unfolding Energy - mRNA 2.30553 kcal/mol@LB@Unfolding Energy - sRNA 0.506316 kcal/mol@LB@@LB@Position - mRNA 123 -- 132@LB@Position - sRNA 80 -- 89@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 80 -- 86@LB@
78	0.01399	0.5385	b3526	kdgK	-7.99	0.228654	189 -- 197	80 -- 88	2-dehydro-3-deoxygluconokinase	_____________188_______198\n_____________\|_________\|\n5'-CCC...AGAUC_________ACUAU...CUU-3'\n______________AGGUUCACG\n______________\|:\|\|\|\|\|\|\|\n______________UUCAAGUGC\n3'-CGC...GCGUU_________AACCG...AAG-5'\n_____________\|_________\|\n_____________89________79\n	191 -- 197	80 -- 86	-11.7911 kcal/mol	3.29177 kcal/mol	0.504555 kcal/mol	188 198@LB@ \| \|@LB@5'-CCC...AGAUC ACUAU...CUU-3'@LB@ AGGUUCACG@LB@ \|:\|\|\|\|\|\|\|@LB@ UUCAAGUGC@LB@3'-CGC...GCGUU AACCG...AAG-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -11.7911 kcal/mol@LB@Unfolding Energy - mRNA 3.29177 kcal/mol@LB@Unfolding Energy - sRNA 0.504555 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 80 -- 86@LB@
197	0.0346	0.5559	b2829	ptsP	-9.94	0.108120	103 -- 113	80 -- 90	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	_____________102_________114\n_____________\|___________\|\n5'-CCA...AAUGA___________AGUGU...UGG-3'\n______________AAGAGUUCGCG\n______________\|\|:\|\|\|\|\|:\|\|\n______________UUUUCAAGUGC\n3'-CGC...AGGCG___________AACCG...AAG-5'\n_____________\|___________\|\n_____________91__________79\n	107 -- 113	80 -- 86	-13.2227 kcal/mol	2.77203 kcal/mol	0.506776 kcal/mol	102 114@LB@ \| \|@LB@5'-CCA...AAUGA AGUGU...UGG-3'@LB@ AAGAGUUCGCG@LB@ \|\|:\|\|\|\|\|:\|\|@LB@ UUUUCAAGUGC@LB@3'-CGC...AGGCG AACCG...AAG-5'@LB@ \| \|@LB@ 91 79@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -13.2227 kcal/mol@LB@Unfolding Energy - mRNA 2.77203 kcal/mol@LB@Unfolding Energy - sRNA 0.506776 kcal/mol@LB@@LB@Position - mRNA 103 -- 113@LB@Position - sRNA 80 -- 90@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 80 -- 86@LB@
155	0.02668	0.5559	b1625	cnu	-8.12	0.218326	240 -- 246	81 -- 87	nucleoid-associated oriC-binding protein; H-NS and StpA stabilizing factor	_____________239_____247\n_____________\|_______\|\n5'-UUU...AAAUC_______UCGAA...AUC-3'\n______________AGUUCAC\n______________\|\|\|\|\|\|\|\n______________UCAAGUG\n3'-CGC...CGUUU_______CAACC...AAG-5'\n_____________\|_______\|\n_____________88______80\n	240 -- 246	81 -- 87	-9.1905 kcal/mol	0.576286 kcal/mol	0.494577 kcal/mol	239 247@LB@ \| \|@LB@5'-UUU...AAAUC UCGAA...AUC-3'@LB@ AGUUCAC@LB@ \|\|\|\|\|\|\|@LB@ UCAAGUG@LB@3'-CGC...CGUUU CAACC...AAG-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.1905 kcal/mol@LB@Unfolding Energy - mRNA 0.576286 kcal/mol@LB@Unfolding Energy - sRNA 0.494577 kcal/mol@LB@@LB@Position - mRNA 240 -- 246@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 81 -- 87@LB@
156	0.02672	0.5559	b0957	ompA	-9.60	0.124024	22 -- 30	81 -- 89	outer membrane protein A (3a;II*;G;d)	_____________21________31\n_____________\|_________\|\n5'-CUU...CUGAC_________ACUUG...AAC-3'\n______________GGAGUUCAC\n______________::\|\|\|\|\|\|\|\n______________UUUCAAGUG\n3'-CGC...GGCGU_________CAACC...AAG-5'\n_____________\|_________\|\n_____________90________80\n	24 -- 30	81 -- 87	-11.1644 kcal/mol	1.067 kcal/mol	0.501582 kcal/mol	21 31@LB@ \| \|@LB@5'-CUU...CUGAC ACUUG...AAC-3'@LB@ GGAGUUCAC@LB@ ::\|\|\|\|\|\|\|@LB@ UUUCAAGUG@LB@3'-CGC...GGCGU CAACC...AAG-5'@LB@ \| \|@LB@ 90 80@LB@@LB@@LB@Energy -9.60 kcal/mol@LB@Hybridization Energy -11.1644 kcal/mol@LB@Unfolding Energy - mRNA 1.067 kcal/mol@LB@Unfolding Energy - sRNA 0.501582 kcal/mol@LB@@LB@Position - mRNA 22 -- 30@LB@Position - sRNA 81 -- 89@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 81 -- 87@LB@
161	0.02817	0.5559	b0852	rimK	-8.21	0.210781	44 -- 79	81 -- 107	ribosomal protein S6 modification protein	_____________43___________________________________80\n_____________\|____________________________________\|\n5'-AAC...CGCCG____A_______CGAUCAU______C___CAA____UAAAG...AUC-3'\n______________GGAU_CCUGGAG_______AUCCGC_GAA___UCAU\n______________\|\|\|\|_\|\|\|\|\|\|\|_______\|\|\|\|\|\|_:\|\|___\|\|\|:\n______________CCUA_GGACCUC_______UAGGCG_UUU___AGUG\n_________3'-CG_________________________U___CA_____CAACC...AAG-5'\n_____________\|____________________________________\|\n_____________108__________________________________80\n	49 -- 55	97 -- 103	-27.5385 kcal/mol	7.46513 kcal/mol	11.8593 kcal/mol	43 80@LB@ \| \|@LB@5'-AAC...CGCCG A CGAUCAU C CAA UAAAG...AUC-3'@LB@ GGAU CCUGGAG AUCCGC GAA UCAU@LB@ \|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\| :\|\| \|\|\|:@LB@ CCUA GGACCUC UAGGCG UUU AGUG@LB@ 3'-CG U CA CAACC...AAG-5'@LB@ \| \|@LB@ 108 80@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -27.5385 kcal/mol@LB@Unfolding Energy - mRNA 7.46513 kcal/mol@LB@Unfolding Energy - sRNA 11.8593 kcal/mol@LB@@LB@Position - mRNA 44 -- 79@LB@Position - sRNA 81 -- 107@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 97 -- 103@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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