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@
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@
193	0.03391	0.5559	b3642	pyrE	-10.20	0.097546	70 -- 90	57 -- 80	orotate phosphoribosyltransferase	_____________69_______________________91\n_____________\|________________________\|\n5'-CGG...AUCUU_______C___CC_______GG__AUCGA...AUU-3'\n______________GUUGGCU_UGG_____CGAG__GA\n______________\|\|\|\|\|\|\|_\|:\|_____\|\|\|\|__\|\|\n______________CAACCGA_AUC_____GCUC__CU\n3'-CGC...AAGUG_______A___AAUAA____AA__CUUUG...AAG-5'\n_____________\|________________________\|\n_____________81_______________________56\n	70 -- 76	74 -- 80	-18.9167 kcal/mol	7.49492 kcal/mol	1.21861 kcal/mol	69 91@LB@ \| \|@LB@5'-CGG...AUCUU C CC GG AUCGA...AUU-3'@LB@ GUUGGCU UGG CGAG GA@LB@ \|\|\|\|\|\|\| \|:\| \|\|\|\| \|\|@LB@ CAACCGA AUC GCUC CU@LB@3'-CGC...AAGUG A AAUAA AA CUUUG...AAG-5'@LB@ \| \|@LB@ 81 56@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -18.9167 kcal/mol@LB@Unfolding Energy - mRNA 7.49492 kcal/mol@LB@Unfolding Energy - sRNA 1.21861 kcal/mol@LB@@LB@Position - mRNA 70 -- 90@LB@Position - sRNA 57 -- 80@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 74 -- 80@LB@
194	0.03409	0.5559	b1836	yebV	-7.98	0.229830	12 -- 23	77 -- 87	uncharacterized protein	_____________11___________24\n_____________\|____________\|\n5'-CCA...GGAUU________A___AAAAA...CUG-3'\n______________GGUUCGCG_UUG\n______________:\|\|\|\|:\|\|_\|\|\|\n______________UCAAGUGC_AAC\n3'-CGC...CGUUU____________CGAAA...AAG-5'\n_____________\|____________\|\n_____________88___________76\n	13 -- 19	80 -- 86	-12.5297 kcal/mol	4.04369 kcal/mol	0.505155 kcal/mol	11 24@LB@ \| \|@LB@5'-CCA...GGAUU A AAAAA...CUG-3'@LB@ GGUUCGCG UUG@LB@ :\|\|\|\|:\|\| \|\|\|@LB@ UCAAGUGC AAC@LB@3'-CGC...CGUUU CGAAA...AAG-5'@LB@ \| \|@LB@ 88 76@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -12.5297 kcal/mol@LB@Unfolding Energy - mRNA 4.04369 kcal/mol@LB@Unfolding Energy - sRNA 0.505155 kcal/mol@LB@@LB@Position - mRNA 12 -- 23@LB@Position - sRNA 77 -- 87@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 80 -- 86@LB@
195	0.03428	0.5559	b0434	yajG	-10.30	0.093744	131 -- 149	66 -- 84	putative lipoprotein	_____________130__________________150\n_____________\|____________________\|\n5'-UGG...UCCCC___C_______AAU______GAUGG...UGC-3'\n______________UCG_CGUUGGC____GUUAU\n______________\|\|:_\|\|\|\|\|\|\|____\|\|\|\|\|\n______________AGU_GCAACCG____CAAUA\n3'-CGC...UUUCA___________AAAU_____AGCUC...AAG-5'\n_____________\|____________________\|\n_____________85___________________65\n	135 -- 141	75 -- 81	-17.0927 kcal/mol	6.21917 kcal/mol	0.5705 kcal/mol	130 150@LB@ \| \|@LB@5'-UGG...UCCCC C AAU GAUGG...UGC-3'@LB@ UCG CGUUGGC GUUAU@LB@ \|\|: \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AGU GCAACCG CAAUA@LB@3'-CGC...UUUCA AAAU AGCUC...AAG-5'@LB@ \| \|@LB@ 85 65@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -17.0927 kcal/mol@LB@Unfolding Energy - mRNA 6.21917 kcal/mol@LB@Unfolding Energy - sRNA 0.5705 kcal/mol@LB@@LB@Position - mRNA 131 -- 149@LB@Position - sRNA 66 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 75 -- 81@LB@
196	0.0344	0.5559	b0954	fabA	-7.50	0.274211	100 -- 110	74 -- 84	beta-hydroxydecanoyl thioester dehydrase	_____________99__________111\n_____________\|___________\|\n5'-GUG...GGCCA___________GAACU...ACA-3'\n______________UUACGUUGGCU\n______________\|:\|\|\|\|\|\|\|\|\|\n______________AGUGCAACCGA\n3'-CGC...UUUCA___________AAUCA...AAG-5'\n_____________\|___________\|\n_____________85__________73\n	104 -- 110	74 -- 80	-16.8122 kcal/mol	8.80896 kcal/mol	0.508159 kcal/mol	99 111@LB@ \| \|@LB@5'-GUG...GGCCA GAACU...ACA-3'@LB@ UUACGUUGGCU@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ AGUGCAACCGA@LB@3'-CGC...UUUCA AAUCA...AAG-5'@LB@ \| \|@LB@ 85 73@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -16.8122 kcal/mol@LB@Unfolding Energy - mRNA 8.80896 kcal/mol@LB@Unfolding Energy - sRNA 0.508159 kcal/mol@LB@@LB@Position - mRNA 100 -- 110@LB@Position - sRNA 74 -- 84@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 74 -- 80@LB@
197	0.0346	0.5559	b2829	ptsP	-9.94	0.108120	103 -- 113	80 -- 90	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	_____________102_________114\n_____________\|___________\|\n5'-CCA...AAUGA___________AGUGU...UGG-3'\n______________AAGAGUUCGCG\n______________\|\|:\|\|\|\|\|:\|\|\n______________UUUUCAAGUGC\n3'-CGC...AGGCG___________AACCG...AAG-5'\n_____________\|___________\|\n_____________91__________79\n	107 -- 113	80 -- 86	-13.2227 kcal/mol	2.77203 kcal/mol	0.506776 kcal/mol	102 114@LB@ \| \|@LB@5'-CCA...AAUGA AGUGU...UGG-3'@LB@ AAGAGUUCGCG@LB@ \|\|:\|\|\|\|\|:\|\|@LB@ UUUUCAAGUGC@LB@3'-CGC...AGGCG AACCG...AAG-5'@LB@ \| \|@LB@ 91 79@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -13.2227 kcal/mol@LB@Unfolding Energy - mRNA 2.77203 kcal/mol@LB@Unfolding Energy - sRNA 0.506776 kcal/mol@LB@@LB@Position - mRNA 103 -- 113@LB@Position - sRNA 80 -- 90@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 80 -- 86@LB@
198	0.03475	0.5559	b1249	clsA	-8.08	0.221640	216 -- 230	57 -- 82	cardiolipin synthase 1	_____________215________________________231\n_____________\|__________________________\|\n5'-GUC...UUUAU__________________________UUGGC...CAG-3'\n______________ACGUUGGU___________GAGUUGG\n______________\|\|\|\|\|\|\|:___________\|\|\|\|\|\|:\n______________UGCAACCG___________CUCAACU\n3'-CGC...UCAAG________AAAUCAAUAAG_______CUUUG...AAG-5'\n_____________\|__________________________\|\n_____________83_________________________56\n	224 -- 230	57 -- 63	-16.5635 kcal/mol	7.18735 kcal/mol	1.29708 kcal/mol	215 231@LB@ \| \|@LB@5'-GUC...UUUAU UUGGC...CAG-3'@LB@ ACGUUGGU GAGUUGG@LB@ \|\|\|\|\|\|\|: \|\|\|\|\|\|:@LB@ UGCAACCG CUCAACU@LB@3'-CGC...UCAAG AAAUCAAUAAG CUUUG...AAG-5'@LB@ \| \|@LB@ 83 56@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -16.5635 kcal/mol@LB@Unfolding Energy - mRNA 7.18735 kcal/mol@LB@Unfolding Energy - sRNA 1.29708 kcal/mol@LB@@LB@Position - mRNA 216 -- 230@LB@Position - sRNA 57 -- 82@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 57 -- 63@LB@
199	0.03481	0.5559	b0407	yajC	-8.41	0.195839	88 -- 104	15 -- 30	SecYEG protein translocase auxillary subunit	_____________87________________105\n_____________\|_________________\|\n5'-UCU...UUACG_____CUAUU_______GUAAA...UUU-3'\n______________CAAGG_____GAAGAGG\n______________\|\|\|\|\|_____:\|\|\|\|\|\|\n______________GUUCC_____UUUCUCC\n3'-CGC...CUGAA_____CAAU________ACGGC...AAG-5'\n_____________\|_________________\|\n_____________31________________14\n	98 -- 104	15 -- 21	-15.1331 kcal/mol	3.4367 kcal/mol	3.28624 kcal/mol	87 105@LB@ \| \|@LB@5'-UCU...UUACG CUAUU GUAAA...UUU-3'@LB@ CAAGG GAAGAGG@LB@ \|\|\|\|\| :\|\|\|\|\|\|@LB@ GUUCC UUUCUCC@LB@3'-CGC...CUGAA CAAU ACGGC...AAG-5'@LB@ \| \|@LB@ 31 14@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -15.1331 kcal/mol@LB@Unfolding Energy - mRNA 3.4367 kcal/mol@LB@Unfolding Energy - sRNA 3.28624 kcal/mol@LB@@LB@Position - mRNA 88 -- 104@LB@Position - sRNA 15 -- 30@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 15 -- 21@LB@
200	0.03481	0.5559	b1058	yceO	-9.40	0.133707	85 -- 100	70 -- 85	uncharacterized protein	_____________84_______________101\n_____________\|________________\|\n5'-CCU...UUAAA_______CA_______GGGAA...GAU-3'\n______________UUUGCGU__GUUUUAG\n______________\|\|::\|\|\|__\|:\|\|\|\|\|\n______________AAGUGCA__CGAAAUC\n3'-CGC...UUUUC_______AC_______AAUAA...AAG-5'\n_____________\|________________\|\n_____________86_______________69\n	94 -- 100	70 -- 76	-11.7699 kcal/mol	1.79867 kcal/mol	0.567379 kcal/mol	84 101@LB@ \| \|@LB@5'-CCU...UUAAA CA GGGAA...GAU-3'@LB@ UUUGCGU GUUUUAG@LB@ \|\|::\|\|\| \|:\|\|\|\|\|@LB@ AAGUGCA CGAAAUC@LB@3'-CGC...UUUUC AC AAUAA...AAG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -11.7699 kcal/mol@LB@Unfolding Energy - mRNA 1.79867 kcal/mol@LB@Unfolding Energy - sRNA 0.567379 kcal/mol@LB@@LB@Position - mRNA 85 -- 100@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 94 -- 100@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching