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
109	0.01118	0.3104	b3195	mlaF	-11.81	0.058997	89 -- 105	1 -- 18	ABC transporter maintaining OM lipid asymmetry ATP-binding protein		_____________88_________________106\n_____________\|__________________\|\n5'-UUU...AGUAA___________AG_____GCUAA...GAG-3'\n______________AACAAAUGC_C__CUUUC\n______________\|\|\|\|\|\|\|\|\|_\|__\|\|\|\|\|\n______________UUGUUUACG_G__GAAAG\n3'-UUU...UACUA_________C_CA_____-5'\n_____________\|_________________\|\n_____________19________________1\n	91 -- 97	10 -- 16	-16.9522 kcal/mol	3.89814 kcal/mol	1.24077 kcal/mol	88 106@LB@ \| \|@LB@5'-UUU...AGUAA AG GCUAA...GAG-3'@LB@ AACAAAUGC C CUUUC@LB@ \|\|\|\|\|\|\|\|\| \| \|\|\|\|\|@LB@ UUGUUUACG G GAAAG@LB@3'-UUU...UACUA C CA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -16.9522 kcal/mol@LB@Unfolding Energy - mRNA 3.89814 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 89 -- 105@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 10 -- 16@LB@
114	0.01161	0.3104	b3392	hofP	-8.60	0.204995	138 -- 147	1 -- 11	DNA catabolic protein		_____________137_________148\n_____________\|___________\|\n5'-ACU...CGUGA___________GUUAA...GCG-3'\n______________GC_CGUUUUUC\n______________\|\|_\|\|\|:\|\|\|\|\n______________CG_GCAGAAAG\n3'-UUU...GUUUA__C________-5'\n_____________\|__________\|\n_____________12_________1\n	141 -- 147	1 -- 7	-12.6405 kcal/mol	2.86562 kcal/mol	1.17076 kcal/mol	137 148@LB@ \| \|@LB@5'-ACU...CGUGA GUUAA...GCG-3'@LB@ GC CGUUUUUC@LB@ \|\| \|\|\|:\|\|\|\|@LB@ CG GCAGAAAG@LB@3'-UUU...GUUUA C -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.6405 kcal/mol@LB@Unfolding Energy - mRNA 2.86562 kcal/mol@LB@Unfolding Energy - sRNA 1.17076 kcal/mol@LB@@LB@Position - mRNA 138 -- 147@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 1 -- 7@LB@
120	0.01222	0.3104	b0916	ycaQ	-9.32	0.156865	225 -- 243	1 -- 17	DUF1006 family protein with C-terminal wHTH domain		_____________224_________________244\n_____________\|___________________\|\n5'-UGG...CCCUU__U_________AAUC___ACCUU...AUA-3'\n______________GC_GAUGCGCGU____UUC\n______________:\|_:\|\|\|\|\|\|\|\|____\|\|\|\n______________UG_UUACGCGCA____AAG\n3'-UUU...ACUAU__U_________GA_____-5'\n_____________\|__________________\|\n_____________18_________________1\n	230 -- 236	6 -- 12	-16.5738 kcal/mol	6.00902 kcal/mol	1.23994 kcal/mol	224 244@LB@ \| \|@LB@5'-UGG...CCCUU U AAUC ACCUU...AUA-3'@LB@ GC GAUGCGCGU UUC@LB@ :\| :\|\|\|\|\|\|\|\| \|\|\|@LB@ UG UUACGCGCA AAG@LB@3'-UUU...ACUAU U GA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -16.5738 kcal/mol@LB@Unfolding Energy - mRNA 6.00902 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 225 -- 243@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 6 -- 12@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@
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@
133	0.01287	0.3104	b3179	rlmE	-8.60	0.205247	24 -- 43	1 -- 17	23S rRNA U2552 2'-O-ribose methyltransferase SAM-dependent		_____________23___________________44\n_____________\|____________________\|\n5'-GCC...CUUGA__________CAGAC_____AGGUG...CCC-3'\n______________GCGGAUGUGC_____CUUUC\n______________:\|::\|\|\|:\|\|_____\|\|\|\|\|\n______________UGUUUACGCG_____GAAAG\n3'-UUU...ACUAU__________CA________-5'\n_____________\|___________________\|\n_____________18__________________1\n	27 -- 33	8 -- 14	-16.3409 kcal/mol	6.50016 kcal/mol	1.23994 kcal/mol	23 44@LB@ \| \|@LB@5'-GCC...CUUGA CAGAC AGGUG...CCC-3'@LB@ GCGGAUGUGC CUUUC@LB@ :\|::\|\|\|:\|\| \|\|\|\|\|@LB@ UGUUUACGCG GAAAG@LB@3'-UUU...ACUAU CA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -16.3409 kcal/mol@LB@Unfolding Energy - mRNA 6.50016 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 24 -- 43@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 8 -- 14@LB@
138	0.01331	0.3104	b2897	sdhE	-11.73	0.060976	261 -- 284	1 -- 21	flavinator of succinate dehydrogenase; antitoxin of CptAB toxin-antitoxin pair		_____________260_______________________285\n_____________\|_________________________\|\n5'-GUA...AACUC____UUU___UC_____________GAACA...ACA-3'\n______________GAUA___CAA__AUGC_CGUUUUUC\n______________\|\|\|\|___\|\|\|__\|\|\|\|_\|\|\|:\|\|\|\|\n______________CUAU___GUU__UACG_GCAGAAAG\n3'-UUU...UACUA____U___________C________-5'\n_____________\|________________________\|\n_____________22_______________________1\n	278 -- 284	1 -- 7	-16.4732 kcal/mol	3.48371 kcal/mol	1.25763 kcal/mol	260 285@LB@ \| \|@LB@5'-GUA...AACUC UUU UC GAACA...ACA-3'@LB@ GAUA CAA AUGC CGUUUUUC@LB@ \|\|\|\| \|\|\| \|\|\|\| \|\|\|:\|\|\|\|@LB@ CUAU GUU UACG GCAGAAAG@LB@3'-UUU...UACUA U C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -16.4732 kcal/mol@LB@Unfolding Energy - mRNA 3.48371 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 261 -- 284@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 1 -- 7@LB@
139	0.01337	0.3104	b1255	yciC	-11.25	0.074167	287 -- 299	1 -- 13	UPF0259 family inner membrane protein		_____________286___________300\n_____________\|_____________\|\n5'-AAU...UUGCU__________A__A-3'\n______________AUGUGCGUUU_UC\n______________\|\|\|:\|\|\|\|:\|_\|\|\n______________UACGCGCAGA_AG\n3'-UUU...UUGUU__________A__-5'\n_____________\|____________\|\n_____________14___________1\n	290 -- 296	4 -- 10	-15.0519 kcal/mol	2.63141 kcal/mol	1.17519 kcal/mol	286 300@LB@ \| \|@LB@5'-AAU...UUGCU A A-3'@LB@ AUGUGCGUUU UC@LB@ \|\|\|:\|\|\|\|:\| \|\|@LB@ UACGCGCAGA AG@LB@3'-UUU...UUGUU A -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -15.0519 kcal/mol@LB@Unfolding Energy - mRNA 2.63141 kcal/mol@LB@Unfolding Energy - sRNA 1.17519 kcal/mol@LB@@LB@Position - mRNA 287 -- 299@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 4 -- 10@LB@
146	0.01406	0.3104	b3831	udp	-7.35	0.318150	153 -- 161	1 -- 9	uridine phosphorylase		_____________152_______162\n_____________\|_________\|\n5'-AUC...GUAAA_________UGCUU...AGA-3'\n______________GUGUCUUUU\n______________\|:\|\|\|\|\|\|:\n______________CGCAGAAAG\n3'-UUU...UUACG_________-5'\n_____________\|________\|\n_____________10_______1\n	155 -- 161	1 -- 7	-10.4616 kcal/mol	1.99462 kcal/mol	1.11751 kcal/mol	152 162@LB@ \| \|@LB@5'-AUC...GUAAA UGCUU...AGA-3'@LB@ GUGUCUUUU@LB@ \|:\|\|\|\|\|\|:@LB@ CGCAGAAAG@LB@3'-UUU...UUACG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -10.4616 kcal/mol@LB@Unfolding Energy - mRNA 1.99462 kcal/mol@LB@Unfolding Energy - sRNA 1.11751 kcal/mol@LB@@LB@Position - mRNA 153 -- 161@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 1 -- 7@LB@
155	0.0146	0.3104	b2614	grpE	-10.46	0.101070	105 -- 125	1 -- 22	heat shock protein		_____________104____________________126\n_____________\|______________________\|\n5'-GAG...AAGAU______________A__GC___CCUUG...CUG-3'\n______________UGAUGACAA_UGUG_GU__UUC\n______________\|\|\|\|:\|\|\|\|_\|\|:\|_\|\|__\|\|\|\n______________ACUAUUGUU_ACGC_CA__AAG\n3'-UUU...CUACU_________U____G__GA___-5'\n_____________\|_____________________\|\n_____________23____________________1\n	107 -- 113	14 -- 20	-17.1017 kcal/mol	5.37697 kcal/mol	1.25963 kcal/mol	104 126@LB@ \| \|@LB@5'-GAG...AAGAU A GC CCUUG...CUG-3'@LB@ UGAUGACAA UGUG GU UUC@LB@ \|\|\|\|:\|\|\|\| \|\|:\| \|\| \|\|\|@LB@ ACUAUUGUU ACGC CA AAG@LB@3'-UUU...CUACU U G GA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -17.1017 kcal/mol@LB@Unfolding Energy - mRNA 5.37697 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 105 -- 125@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 107 -- 113@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)

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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