Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
192	0.04008	0.6177	b2822	recC	-5.02	0.370915	179 -- 195	44 -- 57	exonuclease V (RecBCD complex) gamma chain	_____________178_______________196\n_____________\|_________________\|\n5'-AGU...CCGAA_______U__UC_____CCGCU...AGA-3'\n______________UCGUCAG_AG__AGGAG\n______________:\|\|\|\|\|:_\|\|__\|\|\|\|:\n______________GGCAGUU_UC__UCCUU\n3'-UUU...AACCG_________________AAAGU...ACA-5'\n_____________\|_________________\|\n_____________58________________43\n	179 -- 185	51 -- 57	-11.1502 kcal/mol	3.39036 kcal/mol	2.73756 kcal/mol	178 196@LB@ \| \|@LB@5'-AGU...CCGAA U UC CCGCU...AGA-3'@LB@ UCGUCAG AG AGGAG@LB@ :\|\|\|\|\|: \|\| \|\|\|\|:@LB@ GGCAGUU UC UCCUU@LB@3'-UUU...AACCG AAAGU...ACA-5'@LB@ \| \|@LB@ 58 43@LB@@LB@@LB@Energy -5.02 kcal/mol@LB@Hybridization Energy -11.1502 kcal/mol@LB@Unfolding Energy - mRNA 3.39036 kcal/mol@LB@Unfolding Energy - sRNA 2.73756 kcal/mol@LB@@LB@Position - mRNA 179 -- 195@LB@Position - sRNA 44 -- 57@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 51 -- 57@LB@
137	0.02646	0.6177	b3807	cyaY	-4.99	0.375460	213 -- 221	38 -- 46	iron-dependent inhibitor of iron-sulfur cluster formation; frataxin; iron-binding and oxidizing protein	_____________212_______222\n_____________\|_________\|\n5'-UGA...ACAGU_________CGCCU...AAA-3'\n______________GAAUUUCAU\n______________\|\|\|\|\|\|\|\|\|\n______________CUUAAAGUA\n3'-UUU...UUCUC_________AAAAA...ACA-5'\n_____________\|_________\|\n_____________47________37\n	215 -- 221	38 -- 44	-7.89908 kcal/mol	1.90809 kcal/mol	1.00074 kcal/mol	212 222@LB@ \| \|@LB@5'-UGA...ACAGU CGCCU...AAA-3'@LB@ GAAUUUCAU@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUUAAAGUA@LB@3'-UUU...UUCUC AAAAA...ACA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -4.99 kcal/mol@LB@Hybridization Energy -7.89908 kcal/mol@LB@Unfolding Energy - mRNA 1.90809 kcal/mol@LB@Unfolding Energy - sRNA 1.00074 kcal/mol@LB@@LB@Position - mRNA 213 -- 221@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
186	0.03879	0.6177	b2898	ygfZ	-4.98	0.377094	224 -- 230	51 -- 57	iron-sulfur cluster repair protein plumbagin resistance	_____________223_____231\n_____________\|_______\|\n5'-CGU...CCUCC_______CCUAC...CUG-3'\n______________CCGUCAG\n______________\|\|\|\|\|\|:\n______________GGCAGUU\n3'-UUU...AACCG_______UCUCC...ACA-5'\n_____________\|_______\|\n_____________58______50\n	224 -- 230	51 -- 57	-9.02345 kcal/mol	1.32881 kcal/mol	2.71582 kcal/mol	223 231@LB@ \| \|@LB@5'-CGU...CCUCC CCUAC...CUG-3'@LB@ CCGUCAG@LB@ \|\|\|\|\|\|:@LB@ GGCAGUU@LB@3'-UUU...AACCG UCUCC...ACA-5'@LB@ \| \|@LB@ 58 50@LB@@LB@@LB@Energy -4.98 kcal/mol@LB@Hybridization Energy -9.02345 kcal/mol@LB@Unfolding Energy - mRNA 1.32881 kcal/mol@LB@Unfolding Energy - sRNA 2.71582 kcal/mol@LB@@LB@Position - mRNA 224 -- 230@LB@Position - sRNA 51 -- 57@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 51 -- 57@LB@
114	0.02277	0.6177	b4077	gltP	-4.92	0.386213	48 -- 56	47 -- 55	glutamate/aspartate:proton symporter	_____________47________57\n_____________\|_________\|\n5'-GCC...CUGUU_________UUGCG...GCG-3'\n______________GUUAAAGGG\n______________\|\|:\|\|\|\|:\|\n______________CAGUUUCUC\n3'-UUU...CCGGG_________CUUAA...ACA-5'\n_____________\|_________\|\n_____________56________46\n	50 -- 56	47 -- 53	-9.45392 kcal/mol	3.63887 kcal/mol	0.899516 kcal/mol	47 57@LB@ \| \|@LB@5'-GCC...CUGUU UUGCG...GCG-3'@LB@ GUUAAAGGG@LB@ \|\|:\|\|\|\|:\|@LB@ CAGUUUCUC@LB@3'-UUU...CCGGG CUUAA...ACA-5'@LB@ \| \|@LB@ 56 46@LB@@LB@@LB@Energy -4.92 kcal/mol@LB@Hybridization Energy -9.45392 kcal/mol@LB@Unfolding Energy - mRNA 3.63887 kcal/mol@LB@Unfolding Energy - sRNA 0.899516 kcal/mol@LB@@LB@Position - mRNA 48 -- 56@LB@Position - sRNA 47 -- 55@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 47 -- 53@LB@
176	0.03596	0.6177	b1747	astA	-4.82	0.399998	129 -- 139	46 -- 56	arginine succinyltransferase	_____________128_________140\n_____________\|___________\|\n5'-GGC...GUCAG__AA_______UGACG...AAG-3'\n______________CG__GAAGAGG\n______________\|\|__:\|\|\|\|\|\|\n______________GC__UUUCUCC\n3'-UUU...ACCGG__AG_______UUAAA...ACA-5'\n_____________\|___________\|\n_____________57__________45\n	133 -- 139	46 -- 52	-9.86744 kcal/mol	4.11365 kcal/mol	0.93204 kcal/mol	128 140@LB@ \| \|@LB@5'-GGC...GUCAG AA UGACG...AAG-3'@LB@ CG GAAGAGG@LB@ \|\| :\|\|\|\|\|\|@LB@ GC UUUCUCC@LB@3'-UUU...ACCGG AG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -4.82 kcal/mol@LB@Hybridization Energy -9.86744 kcal/mol@LB@Unfolding Energy - mRNA 4.11365 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 129 -- 139@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 46 -- 52@LB@
173	0.03478	0.6177	b1234	rssA	-4.70	0.418234	181 -- 188	43 -- 50	putative patatin-like family phospholipase	_____________180______189\n_____________\|________\|\n5'-GAU...AUUCC________CUUGC...AAA-3'\n______________AGGGGAAU\n______________\|\|:\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	182 -- 188	43 -- 49	-9.05148 kcal/mol	3.5051 kcal/mol	0.845564 kcal/mol	180 189@LB@ \| \|@LB@5'-GAU...AUUCC CUUGC...AAA-3'@LB@ AGGGGAAU@LB@ \|\|:\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -4.70 kcal/mol@LB@Hybridization Energy -9.05148 kcal/mol@LB@Unfolding Energy - mRNA 3.5051 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 181 -- 188@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 43 -- 49@LB@
80	0.01709	0.6177	b2498	upp	-4.70	0.418803	173 -- 195	44 -- 70	uracil phosphoribosyltransferase	_____________172_________________________196\n_____________\|___________________________\|\n5'-GGC...UUUUU___G___________C_______A___AGAGU...CCG-3'\n______________UGU_GCU____GCCC_UCAAAGG_GAA\n______________\|:\|_\|\|\|____\|\|\|\|_\|\|\|\|\|\|:_\|\|\|\n______________AUA_CGA____CGGG_AGUUUCU_CUU\n3'-UUU...CGGUU___G___UAAC____C_______C___AAAGU...ACA-5'\n_____________\|___________________________\|\n_____________71__________________________43\n	185 -- 191	48 -- 54	-22.3772 kcal/mol	6.37003 kcal/mol	11.3101 kcal/mol	172 196@LB@ \| \|@LB@5'-GGC...UUUUU G C A AGAGU...CCG-3'@LB@ UGU GCU GCCC UCAAAGG GAA@LB@ \|:\| \|\|\| \|\|\|\| \|\|\|\|\|\|: \|\|\|@LB@ AUA CGA CGGG AGUUUCU CUU@LB@3'-UUU...CGGUU G UAAC C C AAAGU...ACA-5'@LB@ \| \|@LB@ 71 43@LB@@LB@@LB@Energy -4.70 kcal/mol@LB@Hybridization Energy -22.3772 kcal/mol@LB@Unfolding Energy - mRNA 6.37003 kcal/mol@LB@Unfolding Energy - sRNA 11.3101 kcal/mol@LB@@LB@Position - mRNA 173 -- 195@LB@Position - sRNA 44 -- 70@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 48 -- 54@LB@
166	0.03384	0.6177	b4035	malK	-4.35	0.473183	186 -- 196	44 -- 53	maltose ABC transportor ATPase	_____________185_________197\n_____________\|___________\|\n5'-CGC...UGUUA_______A___GGGCA...UGU-3'\n______________CAAAGGG_GAA\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUUUCUC_CUU\n3'-UUU...GGGCA___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________54__________43\n	186 -- 192	47 -- 53	-9.12531 kcal/mol	3.84302 kcal/mol	0.927997 kcal/mol	185 197@LB@ \| \|@LB@5'-CGC...UGUUA A GGGCA...UGU-3'@LB@ CAAAGGG GAA@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUUUCUC CUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -9.12531 kcal/mol@LB@Unfolding Energy - mRNA 3.84302 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 196@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 47 -- 53@LB@
184	0.03803	0.6177	b3647	ligB	-3.67	0.590336	72 -- 111	39 -- 67	DNA ligase NAD(+)-dependent	_____________71________________________________________112\n_____________\|_________________________________________\|\n5'-GGC...GCUUC_______U________UUCACUGCAAUA____C__U_____GGAAG...AAA-3'\n______________CGC_AUU_GCCUGUCA____________AAGA_GA_UUUCA\n______________\|\|\|_\|\|\|_\|\|\|:\|\|\|\|____________\|\|\|\|_\|\|_\|\|\|\|\|\n______________GCG_UAA_CGGGCAGU____________UUCU_CU_AAAGU\n3'-UUU...UUAUA___A___C________________________C__U_____AAAAA...ACA-5'\n_____________\|_________________________________________\|\n_____________68________________________________________38\n	80 -- 86	52 -- 58	-24.1741 kcal/mol	6.974 kcal/mol	13.5271 kcal/mol	71 112@LB@ \| \|@LB@5'-GGC...GCUUC U UUCACUGCAAUA C U GGAAG...AAA-3'@LB@ CGC AUU GCCUGUCA AAGA GA UUUCA@LB@ \|\|\| \|\|\| \|\|\|:\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|@LB@ GCG UAA CGGGCAGU UUCU CU AAAGU@LB@3'-UUU...UUAUA A C C U AAAAA...ACA-5'@LB@ \| \|@LB@ 68 38@LB@@LB@@LB@Energy -3.67 kcal/mol@LB@Hybridization Energy -24.1741 kcal/mol@LB@Unfolding Energy - mRNA 6.974 kcal/mol@LB@Unfolding Energy - sRNA 13.5271 kcal/mol@LB@@LB@Position - mRNA 72 -- 111@LB@Position - sRNA 39 -- 67@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 52 -- 58@LB@
50	0.009706	0.6129	b0109	nadC	-3.48	0.624399	8 -- 15	22 -- 29	quinolinate phosphoribosyltransferase	_____________7________16\n_____________\|________\|\n____5'-AGGCUAA________ACCAC...AAG-3'\n______________UAUUGUGC\n______________\|\|\|\|:\|\|\|\n______________AUAAUACG\n3'-UUU...AAAUA________GCAGU...ACA-5'\n_____________\|________\|\n_____________30_______21\n	9 -- 15	22 -- 28	-7.42611 kcal/mol	1.02369 kcal/mol	2.92038 kcal/mol	7 16@LB@ \| \|@LB@ 5'-AGGCUAA ACCAC...AAG-3'@LB@ UAUUGUGC@LB@ \|\|\|\|:\|\|\|@LB@ AUAAUACG@LB@3'-UUU...AAAUA GCAGU...ACA-5'@LB@ \| \|@LB@ 30 21@LB@@LB@@LB@Energy -3.48 kcal/mol@LB@Hybridization Energy -7.42611 kcal/mol@LB@Unfolding Energy - mRNA 1.02369 kcal/mol@LB@Unfolding Energy - sRNA 2.92038 kcal/mol@LB@@LB@Position - mRNA 8 -- 15@LB@Position - sRNA 22 -- 29@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 22 -- 28@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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