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
161	0.01501	0.3104	b1709	btuD	-8.32	0.227073	129 -- 137	1 -- 9	vitamin B12 ABC transporter ATPase	_____________128_______138\n_____________\|_________\|\n5'-GCA...AUCCA_________CCCGG...GGC-3'\n______________GCGUUUUUC\n______________\|\|\|\|:\|\|\|\|\n______________CGCAGAAAG\n3'-UUU...UUACG_________-5'\n_____________\|________\|\n_____________10_______1\n	131 -- 137	1 -- 7	-11.771 kcal/mol	2.3321 kcal/mol	1.11751 kcal/mol	128 138@LB@ \| \|@LB@5'-GCA...AUCCA CCCGG...GGC-3'@LB@ GCGUUUUUC@LB@ \|\|\|\|:\|\|\|\|@LB@ CGCAGAAAG@LB@3'-UUU...UUACG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -11.771 kcal/mol@LB@Unfolding Energy - mRNA 2.3321 kcal/mol@LB@Unfolding Energy - sRNA 1.11751 kcal/mol@LB@@LB@Position - mRNA 129 -- 137@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 1 -- 7@LB@
170	0.01687	0.3104	b0033	carB	-11.35	0.071227	1 -- 15	5 -- 17	carbamoyl-phosphate synthase large subunit	______________1______________16\n______________\|______________\|\n___________5'-_____CC________ACGCA...CGU-3'\n______________GCAAA__UGCGUGUC\n______________:\|\|\|\|__\|\|\|\|:\|\|\|\n______________UGUUU__ACGCGCAG\n3'-UUU...ACUAU_______________AAAG-5'\n_____________\|_______________\|\n_____________18______________4\n	9 -- 15	5 -- 11	-15.984 kcal/mol	3.41554 kcal/mol	1.22241 kcal/mol	1 16@LB@ \| \|@LB@ 5'- CC ACGCA...CGU-3'@LB@ GCAAA UGCGUGUC@LB@ :\|\|\|\| \|\|\|\|:\|\|\|@LB@ UGUUU ACGCGCAG@LB@3'-UUU...ACUAU AAAG-5'@LB@ \| \|@LB@ 18 4@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -15.984 kcal/mol@LB@Unfolding Energy - mRNA 3.41554 kcal/mol@LB@Unfolding Energy - sRNA 1.22241 kcal/mol@LB@@LB@Position - mRNA 1 -- 15@LB@Position - sRNA 5 -- 17@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 5 -- 11@LB@
116	0.01184	0.3104	b1218	chaC	-12.45	0.045440	10 -- 29	8 -- 30	cation transport regulator	_____________9_______________________30\n_____________\|_______________________\|\n5'-AUA...GCCAA_______________________AUAAA...CGC-3'\n______________AGGG__GAUGAUGAUAAAUG_GC\n______________\|\|\|\|__\|\|\|\|\|\|:\|:\|\|\|\|\|_\|\|\n______________UCCC__CUACUAUUGUUUAC_CG\n3'-UUU...UUAAG____UA______________G__CAGAAAG-5'\n_____________\|_______________________\|\n_____________31______________________7\n	21 -- 27	11 -- 17	-25.0616 kcal/mol	5.19055 kcal/mol	7.41684 kcal/mol	9 30@LB@ \| \|@LB@5'-AUA...GCCAA AUAAA...CGC-3'@LB@ AGGG GAUGAUGAUAAAUG GC@LB@ \|\|\|\| \|\|\|\|\|\|:\|:\|\|\|\|\| \|\|@LB@ UCCC CUACUAUUGUUUAC CG@LB@3'-UUU...UUAAG UA G CAGAAAG-5'@LB@ \| \|@LB@ 31 7@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -25.0616 kcal/mol@LB@Unfolding Energy - mRNA 5.19055 kcal/mol@LB@Unfolding Energy - sRNA 7.41684 kcal/mol@LB@@LB@Position - mRNA 10 -- 29@LB@Position - sRNA 8 -- 30@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 11 -- 17@LB@
164	0.0157	0.3104	b1735	chbR	-6.99	0.357617	139 -- 145	6 -- 12	repressor of chb operon for N N'-diacetylchitobiose utilization	_____________138_____146\n_____________\|_______\|\n5'-GAU...AUGCU_______GAACU...CUG-3'\n______________UGCGCGU\n______________\|\|\|\|\|\|\|\n______________ACGCGCA\n3'-UUU...UGUUU_______GAAAG-5'\n_____________\|_______\|\n_____________13______5\n	139 -- 145	6 -- 12	-12.5358 kcal/mol	4.43858 kcal/mol	1.10371 kcal/mol	138 146@LB@ \| \|@LB@5'-GAU...AUGCU GAACU...CUG-3'@LB@ UGCGCGU@LB@ \|\|\|\|\|\|\|@LB@ ACGCGCA@LB@3'-UUU...UGUUU GAAAG-5'@LB@ \| \|@LB@ 13 5@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -12.5358 kcal/mol@LB@Unfolding Energy - mRNA 4.43858 kcal/mol@LB@Unfolding Energy - sRNA 1.10371 kcal/mol@LB@@LB@Position - mRNA 139 -- 145@LB@Position - sRNA 6 -- 12@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 6 -- 12@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@
47	0.003448	0.2484	b0614	citX	-10.13	0.115098	76 -- 91	4 -- 17	apo-citrate lyase phosphoribosyl-dephospho-CoA transferase	_____________75_______________92\n_____________\|________________\|\n5'-UUA...GCUGC____AC__________GCUGA...UCA-3'\n______________GCGA__GUGCGCGUCU\n______________:\|:\|__:\|\|\|\|\|\|\|\|\|\n______________UGUU__UACGCGCAGA\n3'-UUU...ACUAU________________AAG-5'\n_____________\|________________\|\n_____________18_______________3\n	85 -- 91	4 -- 10	-19.1919 kcal/mol	7.83057 kcal/mol	1.22888 kcal/mol	75 92@LB@ \| \|@LB@5'-UUA...GCUGC AC GCUGA...UCA-3'@LB@ GCGA GUGCGCGUCU@LB@ :\|:\| :\|\|\|\|\|\|\|\|\|@LB@ UGUU UACGCGCAGA@LB@3'-UUU...ACUAU AAG-5'@LB@ \| \|@LB@ 18 3@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -19.1919 kcal/mol@LB@Unfolding Energy - mRNA 7.83057 kcal/mol@LB@Unfolding Energy - sRNA 1.22888 kcal/mol@LB@@LB@Position - mRNA 76 -- 91@LB@Position - sRNA 4 -- 17@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 4 -- 10@LB@
55	0.005043	0.3024	b1625	cnu	-10.91	0.084723	38 -- 57	1 -- 21	nucleoid-associated oriC-binding protein; H-NS and StpA stabilizing factor	_____________37____________________58\n_____________\|_____________________\|\n5'-UUU...UCAGG_________________AC__UUUUC...AUC-3'\n______________GAUAGUAAA_GCGCGUU__UC\n______________\|\|\|\|::\|\|\|_\|\|\|\|\|\|:__\|\|\n______________CUAUUGUUU_CGCGCAG__AG\n3'-UUU...UACUA_________A_______AA__-5'\n_____________\|____________________\|\n_____________22___________________1\n	47 -- 53	5 -- 11	-17.9355 kcal/mol	5.76636 kcal/mol	1.25763 kcal/mol	37 58@LB@ \| \|@LB@5'-UUU...UCAGG AC UUUUC...AUC-3'@LB@ GAUAGUAAA GCGCGUU UC@LB@ \|\|\|\|::\|\|\| \|\|\|\|\|\|: \|\|@LB@ CUAUUGUUU CGCGCAG AG@LB@3'-UUU...UACUA A AA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -17.9355 kcal/mol@LB@Unfolding Energy - mRNA 5.76636 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 38 -- 57@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 5 -- 11@LB@
86	0.008729	0.3104	b4213	cpdB	-12.03	0.054140	68 -- 81	8 -- 21	2':3'-cyclic-nucleotide 2'-phosphodiesterase	_____________67_____________82\n_____________\|______________\|\n5'-UGA...CUAUC_U____________CAACU...AUA-3'\n______________G_UAAUGAAUGCGC\n______________\|_\|\|\|::\|\|\|\|\|\|\|\n______________C_AUUGUUUACGCG\n3'-UUU...UACUA_U____________CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	75 -- 81	8 -- 14	-15.4826 kcal/mol	2.2212 kcal/mol	1.23638 kcal/mol	67 82@LB@ \| \|@LB@5'-UGA...CUAUC U CAACU...AUA-3'@LB@ G UAAUGAAUGCGC@LB@ \| \|\|\|::\|\|\|\|\|\|\|@LB@ C AUUGUUUACGCG@LB@3'-UUU...UACUA U CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -15.4826 kcal/mol@LB@Unfolding Energy - mRNA 2.2212 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 68 -- 81@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 8 -- 14@LB@
154	0.01456	0.3104	b2048	cpsG	-9.02	0.175967	42 -- 71	4 -- 44	phosphomannomutase	_____________41________________________________________72\n_____________\|_________________________________________\|\n5'-GGG...GGCUC___________GA___________UG_______________CGCGG...GCG-3'\n______________UUAUCUC_GAA_____GGAUGAUG_________GUGCGUUU\n______________\|:\|\|\|\|\|_\|\|\|_____\|\|\|\|\|\|\|\|_________\|:\|\|\|\|:\|\n______________AGUAGAG_CUU_____CCUACUAC_________CGCGCAGA\n3'-UUU...UUUAA_______A___AAGUC________UAUUGUUUA________AAG-5'\n_____________\|_________________________________________\|\n_____________45________________________________________3\n	65 -- 71	4 -- 10	-28.9111 kcal/mol	10.4373 kcal/mol	9.45546 kcal/mol	41 72@LB@ \| \|@LB@5'-GGG...GGCUC GA UG CGCGG...GCG-3'@LB@ UUAUCUC GAA GGAUGAUG GUGCGUUU@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|\|:\|@LB@ AGUAGAG CUU CCUACUAC CGCGCAGA@LB@3'-UUU...UUUAA A AAGUC UAUUGUUUA AAG-5'@LB@ \| \|@LB@ 45 3@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -28.9111 kcal/mol@LB@Unfolding Energy - mRNA 10.4373 kcal/mol@LB@Unfolding Energy - sRNA 9.45546 kcal/mol@LB@@LB@Position - mRNA 42 -- 71@LB@Position - sRNA 4 -- 44@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 4 -- 10@LB@
20	0.0008552	0.1448	b4137	cutA	-9.23	0.162618	220 -- 236	1 -- 16	divalent-cation tolerance protein copper sensitivity	_____________219_______________237\n_____________\|_________________\|\n5'-CAA...AAGUU_____AC_______G__GUGGU...CGG-3'\n______________CGAAU__CGCGUCU_UC\n______________\|:\|\|\|__\|\|\|\|\|\|\|_\|\|\n______________GUUUA__GCGCAGA_AG\n3'-UUU...CUAUU_____C________A__-5'\n_____________\|________________\|\n_____________17_______________1\n	227 -- 233	4 -- 10	-14.9299 kcal/mol	4.46216 kcal/mol	1.23857 kcal/mol	219 237@LB@ \| \|@LB@5'-CAA...AAGUU AC G GUGGU...CGG-3'@LB@ CGAAU CGCGUCU UC@LB@ \|:\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GUUUA GCGCAGA AG@LB@3'-UUU...CUAUU C A -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -14.9299 kcal/mol@LB@Unfolding Energy - mRNA 4.46216 kcal/mol@LB@Unfolding Energy - sRNA 1.23857 kcal/mol@LB@@LB@Position - mRNA 220 -- 236@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 4 -- 10@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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