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
193	0.01896	0.3104	b3181	greA	-10.36	0.105339	194 -- 204	10 -- 20	transcript cleavage factor	_____________193_________205\n_____________\|___________\|\n5'-CGC...GAGGU___________AAGCU...UCG-3'\n______________AUAACAAAUGC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UAUUGUUUACG\n3'-UUU...ACUAC___________CGCAG...AAG-5'\n_____________\|___________\|\n_____________21__________9\n	198 -- 204	10 -- 16	-13.1767 kcal/mol	1.58941 kcal/mol	1.22774 kcal/mol	193 205@LB@ \| \|@LB@5'-CGC...GAGGU AAGCU...UCG-3'@LB@ AUAACAAAUGC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UAUUGUUUACG@LB@3'-UUU...ACUAC CGCAG...AAG-5'@LB@ \| \|@LB@ 21 9@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -13.1767 kcal/mol@LB@Unfolding Energy - mRNA 1.58941 kcal/mol@LB@Unfolding Energy - sRNA 1.22774 kcal/mol@LB@@LB@Position - mRNA 194 -- 204@LB@Position - sRNA 10 -- 20@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 10 -- 16@LB@
23	0.001384	0.1943	b0399	phoB	-10.33	0.106753	53 -- 63	8 -- 18	response regulator in two-component regulatory system with PhoR	_____________52__________64\n_____________\|___________\|\n5'-AGG...ACCCA___________CAUUU...AAG-3'\n______________AACAGAUGUGC\n______________\|\|\|\|:\|\|\|:\|\|\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	57 -- 63	8 -- 14	-14.9736 kcal/mol	3.44457 kcal/mol	1.20363 kcal/mol	52 64@LB@ \| \|@LB@5'-AGG...ACCCA CAUUU...AAG-3'@LB@ AACAGAUGUGC@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -14.9736 kcal/mol@LB@Unfolding Energy - mRNA 3.44457 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 53 -- 63@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 8 -- 14@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@
74	0.006875	0.3087	b2474	tmcA	-10.30	0.108021	196 -- 222	5 -- 31	elongator methionine tRNA (ac4C34) acetyltransferase	_____________195____________________________223\n_____________\|______________________________\|\n5'-GAU...CGGGG_________C___AC____________U__ACACA...UUG-3'\n______________CAGGGAUGG_UGA__UGAC___UGCGC_UC\n______________\|\|\|\|\|\|\|\|:_\|\|\|__\|:\|\|___\|\|\|\|\|_\|\|\n______________GUCCCUACU_ACU__AUUG___ACGCG_AG\n3'-UUU...CUUAA___________________UUU_____C__AAAG-5'\n_____________\|______________________________\|\n_____________32_____________________________4\n	198 -- 204	23 -- 29	-27.934 kcal/mol	9.88036 kcal/mol	7.7585 kcal/mol	195 223@LB@ \| \|@LB@5'-GAU...CGGGG C AC U ACACA...UUG-3'@LB@ CAGGGAUGG UGA UGAC UGCGC UC@LB@ \|\|\|\|\|\|\|\|: \|\|\| \|:\|\| \|\|\|\|\| \|\|@LB@ GUCCCUACU ACU AUUG ACGCG AG@LB@3'-UUU...CUUAA UUU C AAAG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -27.934 kcal/mol@LB@Unfolding Energy - mRNA 9.88036 kcal/mol@LB@Unfolding Energy - sRNA 7.7585 kcal/mol@LB@@LB@Position - mRNA 196 -- 222@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 23 -- 29@LB@
101	0.01005	0.3104	b3288	fmt	-10.27	0.109217	249 -- 255	5 -- 11	10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase	_____________248_____256\n_____________\|_______\|\n5'-AUU...UUGCA_______AUCUC...UGU-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	249 -- 255	5 -- 11	-14.5658 kcal/mol	3.18739 kcal/mol	1.11145 kcal/mol	248 256@LB@ \| \|@LB@5'-AUU...UUGCA AUCUC...UGU-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -14.5658 kcal/mol@LB@Unfolding Energy - mRNA 3.18739 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 249 -- 255@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 5 -- 11@LB@
190	0.01867	0.3104	b0196	rcsF	-10.27	0.109081	201 -- 211	2 -- 13	putative outer membrane protein	_____________200__________212\n_____________\|____________\|\n5'-AAU...AUACU____________ACCGA...AGC-3'\n______________AUGCGUG_CUUU\n______________\|\|\|\|\|:\|_\|\|\|\|\n______________UACGCGC_GAAA\n3'-UUU...UUGUU_______A____G-5'\n_____________\|____________\|\n_____________14___________1\n	201 -- 207	7 -- 13	-12.8527 kcal/mol	1.40833 kcal/mol	1.17421 kcal/mol	200 212@LB@ \| \|@LB@5'-AAU...AUACU ACCGA...AGC-3'@LB@ AUGCGUG CUUU@LB@ \|\|\|\|\|:\| \|\|\|\|@LB@ UACGCGC GAAA@LB@3'-UUU...UUGUU A G-5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -12.8527 kcal/mol@LB@Unfolding Energy - mRNA 1.40833 kcal/mol@LB@Unfolding Energy - sRNA 1.17421 kcal/mol@LB@@LB@Position - mRNA 201 -- 211@LB@Position - sRNA 2 -- 13@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 7 -- 13@LB@
112	0.01125	0.3104	b2515	ispG	-10.24	0.110168	132 -- 140	4 -- 12	1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase	_____________131_______141\n_____________\|_________\|\n5'-CGU...CAGGU_________GACCC...UGA-3'\n______________UGCGCGUCU\n______________\|\|\|\|\|\|\|\|\|\n______________ACGCGCAGA\n3'-UUU...UGUUU_________AAG-5'\n_____________\|_________\|\n_____________13________3\n	134 -- 140	4 -- 10	-16.4542 kcal/mol	5.04928 kcal/mol	1.16019 kcal/mol	131 141@LB@ \| \|@LB@5'-CGU...CAGGU GACCC...UGA-3'@LB@ UGCGCGUCU@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGCGCAGA@LB@3'-UUU...UGUUU AAG-5'@LB@ \| \|@LB@ 13 3@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -16.4542 kcal/mol@LB@Unfolding Energy - mRNA 5.04928 kcal/mol@LB@Unfolding Energy - sRNA 1.16019 kcal/mol@LB@@LB@Position - mRNA 132 -- 140@LB@Position - sRNA 4 -- 12@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 4 -- 10@LB@
166	0.01595	0.3104	b3560	glyQ	-10.24	0.110293	22 -- 29	7 -- 14	glycine tRNA synthetase alpha subunit	_____________21_______30\n_____________\|________\|\n5'-ACA...UAUGA________GUUAU...UGG-3'\n______________AAUGCGCG\n______________\|\|\|\|\|\|\|\|\n______________UUACGCGC\n3'-UUU...AUUGU________AGAAAG-5'\n_____________\|________\|\n_____________15_______6\n	23 -- 29	7 -- 13	-12.7168 kcal/mol	1.35517 kcal/mol	1.11978 kcal/mol	21 30@LB@ \| \|@LB@5'-ACA...UAUGA GUUAU...UGG-3'@LB@ AAUGCGCG@LB@ \|\|\|\|\|\|\|\|@LB@ UUACGCGC@LB@3'-UUU...AUUGU AGAAAG-5'@LB@ \| \|@LB@ 15 6@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -12.7168 kcal/mol@LB@Unfolding Energy - mRNA 1.35517 kcal/mol@LB@Unfolding Energy - sRNA 1.11978 kcal/mol@LB@@LB@Position - mRNA 22 -- 29@LB@Position - sRNA 7 -- 14@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 7 -- 13@LB@
49	0.004401	0.299	b0093	ftsQ	-10.19	0.112476	259 -- 274	4 -- 20	divisome assembly protein membrane anchored protein involved in growth of wall at septum	_____________258_______________275\n_____________\|_________________\|\n5'-GCU...CCGCA________A________GGCGG...CCG-3'\n______________AUAAUGGA__CGCGUCU\n______________\|\|\|\|:::\|__\|\|\|\|\|\|\|\n______________UAUUGUUU__GCGCAGA\n3'-UUU...ACUAC________AC_______AAG-5'\n_____________\|_________________\|\n_____________21________________3\n	268 -- 274	4 -- 10	-13.8485 kcal/mol	2.40331 kcal/mol	1.25368 kcal/mol	258 275@LB@ \| \|@LB@5'-GCU...CCGCA A GGCGG...CCG-3'@LB@ AUAAUGGA CGCGUCU@LB@ \|\|\|\|:::\| \|\|\|\|\|\|\|@LB@ UAUUGUUU GCGCAGA@LB@3'-UUU...ACUAC AC AAG-5'@LB@ \| \|@LB@ 21 3@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -13.8485 kcal/mol@LB@Unfolding Energy - mRNA 2.40331 kcal/mol@LB@Unfolding Energy - sRNA 1.25368 kcal/mol@LB@@LB@Position - mRNA 259 -- 274@LB@Position - sRNA 4 -- 20@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 4 -- 10@LB@
194	0.0191	0.3104	b2698	recX	-10.17	0.113250	93 -- 107	8 -- 22	regulatory protein for RecA	_____________92______________108\n_____________\|_______________\|\n5'-AAA...GUAGA__________G____AGCAG...GAC-3'\n______________UGAUAGCGAA_GCGU\n______________\|\|\|\|\|:\|:\|\|_\|\|\|:\n______________ACUAUUGUUU_CGCG\n3'-UUU...CUACU__________A____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	96 -- 102	13 -- 19	-16.2974 kcal/mol	4.88496 kcal/mol	1.23838 kcal/mol	92 108@LB@ \| \|@LB@5'-AAA...GUAGA G AGCAG...GAC-3'@LB@ UGAUAGCGAA GCGU@LB@ \|\|\|\|\|:\|:\|\| \|\|\|:@LB@ ACUAUUGUUU CGCG@LB@3'-UUU...CUACU A CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -16.2974 kcal/mol@LB@Unfolding Energy - mRNA 4.88496 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 93 -- 107@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 96 -- 102@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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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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