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
191	0.03353	0.5559	b2129	yehX	-7.36	0.287226	59 -- 67	69 -- 77	putative ABC transporter ATPase	_____________58________68\n_____________\|_________\|\n5'-GGU...CAGGC_________GCGCU...UUG-3'\n______________GGUUUUGGU\n______________\|\|:\|\|\|:\|\|\n______________CCGAAAUCA\n3'-CGC...UGCAA_________AUAAG...AAG-5'\n_____________\|_________\|\n_____________78________68\n	61 -- 67	69 -- 75	-10.3561 kcal/mol	2.74802 kcal/mol	0.243235 kcal/mol	58 68@LB@ \| \|@LB@5'-GGU...CAGGC GCGCU...UUG-3'@LB@ GGUUUUGGU@LB@ \|\|:\|\|\|:\|\|@LB@ CCGAAAUCA@LB@3'-CGC...UGCAA AUAAG...AAG-5'@LB@ \| \|@LB@ 78 68@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -10.3561 kcal/mol@LB@Unfolding Energy - mRNA 2.74802 kcal/mol@LB@Unfolding Energy - sRNA 0.243235 kcal/mol@LB@@LB@Position - mRNA 59 -- 67@LB@Position - sRNA 69 -- 77@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 69 -- 75@LB@
189	0.03342	0.5559	b2172	yeiQ	-17.65	0.004645	282 -- 298	70 -- 86	putative NAD-dependent D-mannonate oxidoreductase	_____________281_______________299\n_____________\|_________________\|\n5'-GAU...GUAUC______U__________AG-3'\n______________GUUCAU_UUGGCUUUGG\n______________\|\|\|\|\|:_\|\|\|\|\|\|\|\|:\|\n______________CAAGUG_AACCGAAAUC\n3'-CGC...GUUUU______C__________AAUAA...AAG-5'\n_____________\|_________________\|\n_____________87________________69\n	292 -- 298	70 -- 76	-21.6632 kcal/mol	3.44897 kcal/mol	0.568254 kcal/mol	281 299@LB@ \| \|@LB@5'-GAU...GUAUC U AG-3'@LB@ GUUCAU UUGGCUUUGG@LB@ \|\|\|\|\|: \|\|\|\|\|\|\|\|:\|@LB@ CAAGUG AACCGAAAUC@LB@3'-CGC...GUUUU C AAUAA...AAG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -17.65 kcal/mol@LB@Hybridization Energy -21.6632 kcal/mol@LB@Unfolding Energy - mRNA 3.44897 kcal/mol@LB@Unfolding Energy - sRNA 0.568254 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 70 -- 76@LB@
192	0.03364	0.5559	b2333	yfcP	-8.48	0.190877	22 -- 36	61 -- 77	putative fimbrial-like adhesin protein	_____________21________________37\n_____________\|_________________\|\n5'-GCA...UACCC_________A_______CUUCA...AUU-3'\n______________GGUUUUGGU___UCGAG\n______________\|\|:\|\|\|:\|\|___\|\|\|\|\|\n______________CCGAAAUCA___AGCUC\n3'-CGC...UGCAA_________AUA_____AACUC...AAG-5'\n_____________\|_________________\|\n_____________78________________60\n	23 -- 29	70 -- 76	-16.4218 kcal/mol	7.14733 kcal/mol	0.796269 kcal/mol	21 37@LB@ \| \|@LB@5'-GCA...UACCC A CUUCA...AUU-3'@LB@ GGUUUUGGU UCGAG@LB@ \|\|:\|\|\|:\|\| \|\|\|\|\|@LB@ CCGAAAUCA AGCUC@LB@3'-CGC...UGCAA AUA AACUC...AAG-5'@LB@ \| \|@LB@ 78 60@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -16.4218 kcal/mol@LB@Unfolding Energy - mRNA 7.14733 kcal/mol@LB@Unfolding Energy - sRNA 0.796269 kcal/mol@LB@@LB@Position - mRNA 22 -- 36@LB@Position - sRNA 61 -- 77@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 70 -- 76@LB@
45	0.009513	0.5385	b2513	yfgM	-9.58	0.124672	177 -- 189	15 -- 27	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________176___________190\n_____________\|_____________\|\n5'-GGC...UUACU_________A___AGAAG...UUG-3'\n______________GGGUUAAGG_AGG\n______________\|\|\|\|\|\|\|::_\|\|\|\n______________CCCAAUUUU_UCC\n3'-CGC...AAGUU_________C___ACGGC...AAG-5'\n_____________\|_____________\|\n_____________28____________14\n	179 -- 185	19 -- 25	-14.0675 kcal/mol	1.24912 kcal/mol	3.23583 kcal/mol	176 190@LB@ \| \|@LB@5'-GGC...UUACU A AGAAG...UUG-3'@LB@ GGGUUAAGG AGG@LB@ \|\|\|\|\|\|\|:: \|\|\|@LB@ CCCAAUUUU UCC@LB@3'-CGC...AAGUU C ACGGC...AAG-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -9.58 kcal/mol@LB@Hybridization Energy -14.0675 kcal/mol@LB@Unfolding Energy - mRNA 1.24912 kcal/mol@LB@Unfolding Energy - sRNA 3.23583 kcal/mol@LB@@LB@Position - mRNA 177 -- 189@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 19 -- 25@LB@
123	0.02095	0.5385	b2562	yfhL	-10.74	0.078719	174 -- 195	59 -- 77	putative 4Fe-4S cluster-containing protein	_____________173____________________196\n_____________\|______________________\|\n5'-AGC...CGCCC_____GU_______UGA_____UCCUU...UUA-3'\n______________GGUUU__GUUGUUU___GAGUU\n______________\|\|:\|\|__\|\|\|:\|\|:___\|\|\|\|\|\n______________CCGAA__CAAUAAG___CUCAA\n3'-CGC...UGCAA_____AU_______________CUCUU...AAG-5'\n_____________\|______________________\|\n_____________78_____________________58\n	181 -- 187	64 -- 70	-15.8972 kcal/mol	4.34594 kcal/mol	0.811926 kcal/mol	173 196@LB@ \| \|@LB@5'-AGC...CGCCC GU UGA UCCUU...UUA-3'@LB@ GGUUU GUUGUUU GAGUU@LB@ \|\|:\|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ CCGAA CAAUAAG CUCAA@LB@3'-CGC...UGCAA AU CUCUU...AAG-5'@LB@ \| \|@LB@ 78 58@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -15.8972 kcal/mol@LB@Unfolding Energy - mRNA 4.34594 kcal/mol@LB@Unfolding Energy - sRNA 0.811926 kcal/mol@LB@@LB@Position - mRNA 174 -- 195@LB@Position - sRNA 59 -- 77@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 64 -- 70@LB@
106	0.01861	0.5385	b2754	ygbF	-9.88	0.110684	283 -- 300	13 -- 30	CRISPR adaptation ssRNA endonuclease	_____________282_______________300\n_____________\|_________________\|\n5'-UGG...ACGUG_______AUAUGU_____-3'\n______________CAGGGGU______AGGUG\n______________\|\|:\|\|\|\|______\|\|\|\|\|\n______________GUUCCCA______UCCAC\n3'-CGC...CUGAA_______AUUUUC_____GGCGA...AAG-5'\n_____________\|__________________\|\n_____________31_________________12\n	283 -- 289	24 -- 30	-16.4011 kcal/mol	3.18452 kcal/mol	3.3319 kcal/mol	282 300@LB@ \| \|@LB@5'-UGG...ACGUG AUAUGU -3'@LB@ CAGGGGU AGGUG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ GUUCCCA UCCAC@LB@3'-CGC...CUGAA AUUUUC GGCGA...AAG-5'@LB@ \| \|@LB@ 31 12@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -16.4011 kcal/mol@LB@Unfolding Energy - mRNA 3.18452 kcal/mol@LB@Unfolding Energy - sRNA 3.3319 kcal/mol@LB@@LB@Position - mRNA 283 -- 300@LB@Position - sRNA 13 -- 30@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 24 -- 30@LB@
173	0.03066	0.5559	b2928	yggC	-11.87	0.049837	290 -- 298	75 -- 83	putative PanK family P-loop kinase	_____________289_______299\n_____________\|_________\|\n5'-GAA...CUGCA_________GG-3'\n______________CAUGUUGGC\n______________\|\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	292 -- 298	75 -- 81	-14.124 kcal/mol	1.76242 kcal/mol	0.492259 kcal/mol	289 299@LB@ \| \|@LB@5'-GAA...CUGCA GG-3'@LB@ CAUGUUGGC@LB@ \|\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -14.124 kcal/mol@LB@Unfolding Energy - mRNA 1.76242 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 290 -- 298@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 75 -- 81@LB@
88	0.01545	0.5385	b3009	yghB	-9.13	0.148475	202 -- 216	61 -- 78	general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter	_____________201________________217\n_____________\|__________________\|\n5'-UCU...GUCCA_______________A__AUAUC...UUG-3'\n______________UGGCU___GUUAUUC_AG\n______________\|\|\|\|\|___\|\|\|\|\|\|\|_\|\|\n______________ACCGA___CAAUAAG_UC\n3'-CGC...GUGCA_____AAU_______C__AACUC...AAG-5'\n_____________\|__________________\|\n_____________79_________________60\n	207 -- 213	64 -- 70	-14.1767 kcal/mol	4.24529 kcal/mol	0.796888 kcal/mol	201 217@LB@ \| \|@LB@5'-UCU...GUCCA A AUAUC...UUG-3'@LB@ UGGCU GUUAUUC AG@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ ACCGA CAAUAAG UC@LB@3'-CGC...GUGCA AAU C AACUC...AAG-5'@LB@ \| \|@LB@ 79 60@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -14.1767 kcal/mol@LB@Unfolding Energy - mRNA 4.24529 kcal/mol@LB@Unfolding Energy - sRNA 0.796888 kcal/mol@LB@@LB@Position - mRNA 202 -- 216@LB@Position - sRNA 61 -- 78@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 64 -- 70@LB@
144	0.02429	0.5467	b3156	yhbS	-10.71	0.079718	207 -- 222	50 -- 67	GNAT family putative N-acetyltransferase	_____________206________________223\n_____________\|__________________\|\n5'-CCG...UGCUA__________________CCAUU...AUC-3'\n______________AUUCGAGU__AGAAAUUC\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|:\|\|\n______________UAAGCUCA__UCUUUGAG\n3'-CGC...AUCAA________AC________AGCUU...AAG-5'\n_____________\|__________________\|\n_____________68_________________49\n	216 -- 222	50 -- 56	-17.6544 kcal/mol	2.73618 kcal/mol	4.21029 kcal/mol	206 223@LB@ \| \|@LB@5'-CCG...UGCUA CCAUU...AUC-3'@LB@ AUUCGAGU AGAAAUUC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\|@LB@ UAAGCUCA UCUUUGAG@LB@3'-CGC...AUCAA AC AGCUU...AAG-5'@LB@ \| \|@LB@ 68 49@LB@@LB@@LB@Energy -10.71 kcal/mol@LB@Hybridization Energy -17.6544 kcal/mol@LB@Unfolding Energy - mRNA 2.73618 kcal/mol@LB@Unfolding Energy - sRNA 4.21029 kcal/mol@LB@@LB@Position - mRNA 207 -- 222@LB@Position - sRNA 50 -- 67@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
100	0.01671	0.5385	b3211	yhcC	-9.80	0.114390	283 -- 295	70 -- 82	putative Fe-S oxidoreductase Radical SAM superfamily protein	_____________282___________296\n_____________\|_____________\|\n5'-UGC...GCUGC___GC________CUGCC-3'\n______________ACG__GGUUUUAG\n______________\|\|\|__\|\|:\|\|\|\|\|\n______________UGC__CCGAAAUC\n3'-CGC...UCAAG___AA________AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	289 -- 295	70 -- 76	-11.7424 kcal/mol	1.55142 kcal/mol	0.389672 kcal/mol	282 296@LB@ \| \|@LB@5'-UGC...GCUGC GC CUGCC-3'@LB@ ACG GGUUUUAG@LB@ \|\|\| \|\|:\|\|\|\|\|@LB@ UGC CCGAAAUC@LB@3'-CGC...UCAAG AA AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -9.80 kcal/mol@LB@Hybridization Energy -11.7424 kcal/mol@LB@Unfolding Energy - mRNA 1.55142 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 70 -- 76@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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