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
157	0.02703	0.5559	b3221	yhcH	-9.14	0.148013	119 -- 127	77 -- 85	DUF386 family protein cupin superfamily	_____________118_______128\n_____________\|_________\|\n5'-AUC...GGCAU_________AUUUA...AAG-3'\n______________UUCAUGUUG\n______________\|\|\|\|:\|\|\|\|\n______________AAGUGCAAC\n3'-CGC...UUUUC_________CGAAA...AAG-5'\n_____________\|_________\|\n_____________86________76\n	121 -- 127	77 -- 83	-10.7393 kcal/mol	1.16925 kcal/mol	0.427568 kcal/mol	118 128@LB@ \| \|@LB@5'-AUC...GGCAU AUUUA...AAG-3'@LB@ UUCAUGUUG@LB@ \|\|\|\|:\|\|\|\|@LB@ AAGUGCAAC@LB@3'-CGC...UUUUC CGAAA...AAG-5'@LB@ \| \|@LB@ 86 76@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.16925 kcal/mol@LB@Unfolding Energy - sRNA 0.427568 kcal/mol@LB@@LB@Position - mRNA 119 -- 127@LB@Position - sRNA 77 -- 85@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 77 -- 83@LB@
28	0.005203	0.5385	b3308	rplE	-12.95	0.031988	121 -- 134	62 -- 77	50S ribosomal subunit protein L5	_____________120______________135\n_____________\|________________\|\n5'-AAA...GUGUA________________AGACG...AGA-3'\n______________GGCUUUAG__AUUCGA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\n______________CCGAAAUC__UAAGCU\n3'-CGC...UGCAA________AA______CAACU...AAG-5'\n_____________\|________________\|\n_____________78_______________61\n	122 -- 128	70 -- 76	-17.2589 kcal/mol	3.56808 kcal/mol	0.736118 kcal/mol	120 135@LB@ \| \|@LB@5'-AAA...GUGUA AGACG...AGA-3'@LB@ GGCUUUAG AUUCGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CCGAAAUC UAAGCU@LB@3'-CGC...UGCAA AA CAACU...AAG-5'@LB@ \| \|@LB@ 78 61@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -17.2589 kcal/mol@LB@Unfolding Energy - mRNA 3.56808 kcal/mol@LB@Unfolding Energy - sRNA 0.736118 kcal/mol@LB@@LB@Position - mRNA 121 -- 134@LB@Position - sRNA 62 -- 77@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 70 -- 76@LB@
71	0.01305	0.5385	b3843	ubiD	-10.23	0.096580	123 -- 132	80 -- 89	3-octaprenyl-4-hydroxybenzoate decarboxylase	_____________122________133\n_____________\|__________\|\n5'-CGC...CCGUC__________CUAAU...UGG-3'\n______________AGAGUUCACG\n______________\|:\|\|\|\|\|\|\|\|\n______________UUUCAAGUGC\n3'-CGC...GGCGU__________AACCG...AAG-5'\n_____________\|__________\|\n_____________90_________79\n	126 -- 132	80 -- 86	-13.04 kcal/mol	2.30553 kcal/mol	0.506316 kcal/mol	122 133@LB@ \| \|@LB@5'-CGC...CCGUC CUAAU...UGG-3'@LB@ AGAGUUCACG@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUUCAAGUGC@LB@3'-CGC...GGCGU AACCG...AAG-5'@LB@ \| \|@LB@ 90 79@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -13.04 kcal/mol@LB@Unfolding Energy - mRNA 2.30553 kcal/mol@LB@Unfolding Energy - sRNA 0.506316 kcal/mol@LB@@LB@Position - mRNA 123 -- 132@LB@Position - sRNA 80 -- 89@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 80 -- 86@LB@
149	0.0249	0.5467	b0737	tolQ	-11.44	0.059241	123 -- 143	57 -- 77	membrane spanning protein in TolA-TolQ-TolR complex	_____________122___________________144\n_____________\|_____________________\|\n5'-GCA...GCAGA____C__________C_____CCCAC...CCA-3'\n______________GGUU_UGGUUGUUUG_GUUGA\n______________\|\|:\|_\|:\|\|\|:\|\|:\|_\|\|\|\|\|\n______________CCGA_AUCAAUAAGC_CAACU\n3'-CGC...UGCAA____A__________U_____CUUUG...AAG-5'\n_____________\|_____________________\|\n_____________78____________________56\n	130 -- 136	64 -- 70	-20.7122 kcal/mol	8.05008 kcal/mol	1.21841 kcal/mol	122 144@LB@ \| \|@LB@5'-GCA...GCAGA C C CCCAC...CCA-3'@LB@ GGUU UGGUUGUUUG GUUGA@LB@ \|\|:\| \|:\|\|\|:\|\|:\| \|\|\|\|\|@LB@ CCGA AUCAAUAAGC CAACU@LB@3'-CGC...UGCAA A U CUUUG...AAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -20.7122 kcal/mol@LB@Unfolding Energy - mRNA 8.05008 kcal/mol@LB@Unfolding Energy - sRNA 1.21841 kcal/mol@LB@@LB@Position - mRNA 123 -- 143@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 64 -- 70@LB@
38	0.006978	0.5385	b3738	atpB	-10.53	0.085759	128 -- 143	69 -- 84	F0 sector of membrane-bound ATP synthase subunit a	_____________127______________144\n_____________\|________________\|\n5'-CAU...GAUCG______G_________GCUGG...ACC-3'\n______________UUACGU_GGUUUUGGU\n______________\|:\|\|\|\|_\|\|:\|\|\|:\|\|\n______________AGUGCA_CCGAAAUCA\n3'-CGC...UUUCA______A_________AUAAG...AAG-5'\n_____________\|________________\|\n_____________85_______________68\n	137 -- 143	69 -- 75	-16.8893 kcal/mol	5.79988 kcal/mol	0.563592 kcal/mol	127 144@LB@ \| \|@LB@5'-CAU...GAUCG G GCUGG...ACC-3'@LB@ UUACGU GGUUUUGGU@LB@ \|:\|\|\|\| \|\|:\|\|\|:\|\|@LB@ AGUGCA CCGAAAUCA@LB@3'-CGC...UUUCA A AUAAG...AAG-5'@LB@ \| \|@LB@ 85 68@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -16.8893 kcal/mol@LB@Unfolding Energy - mRNA 5.79988 kcal/mol@LB@Unfolding Energy - sRNA 0.563592 kcal/mol@LB@@LB@Position - mRNA 128 -- 143@LB@Position - sRNA 69 -- 84@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 69 -- 75@LB@
61	0.01179	0.5385	b3748	rbsD	-10.58	0.083988	129 -- 141	72 -- 84	D-ribose pyranase	_____________128___________142\n_____________\|_____________\|\n5'-GGU...UAACG_____A_______CCCAA...UCC-3'\n______________UCACG_UGGUUUU\n______________\|\|\|\|\|_\|\|\|:\|\|\|\n______________AGUGC_ACCGAAA\n3'-CGC...UUUCA_____A_______UCAAU...AAG-5'\n_____________\|_____________\|\n_____________85____________71\n	135 -- 141	72 -- 78	-14.1499 kcal/mol	3.06287 kcal/mol	0.509125 kcal/mol	128 142@LB@ \| \|@LB@5'-GGU...UAACG A CCCAA...UCC-3'@LB@ UCACG UGGUUUU@LB@ \|\|\|\|\| \|\|\|:\|\|\|@LB@ AGUGC ACCGAAA@LB@3'-CGC...UUUCA A UCAAU...AAG-5'@LB@ \| \|@LB@ 85 71@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -14.1499 kcal/mol@LB@Unfolding Energy - mRNA 3.06287 kcal/mol@LB@Unfolding Energy - sRNA 0.509125 kcal/mol@LB@@LB@Position - mRNA 129 -- 141@LB@Position - sRNA 72 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 72 -- 78@LB@
118	0.01985	0.5385	b2318	truA	-10.16	0.099312	131 -- 143	70 -- 82	tRNA pseudouridine(38-40) synthase	_____________130___________144\n_____________\|_____________\|\n5'-GUG...CGAUA_____C_______CGGCG...GCA-3'\n______________ACGUU_GCUUUGG\n______________\|\|\|\|\|_\|\|\|\|\|:\|\n______________UGCAA_CGAAAUC\n3'-CGC...UCAAG_____C_______AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	137 -- 143	70 -- 76	-13.1761 kcal/mol	2.62838 kcal/mol	0.389672 kcal/mol	130 144@LB@ \| \|@LB@5'-GUG...CGAUA C CGGCG...GCA-3'@LB@ ACGUU GCUUUGG@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ UGCAA CGAAAUC@LB@3'-CGC...UCAAG C AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -13.1761 kcal/mol@LB@Unfolding Energy - mRNA 2.62838 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 131 -- 143@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 70 -- 76@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@
55	0.01095	0.5385	b1220	ychO	-5.56	0.517016	132 -- 175	64 -- 91	putative invasin	_____________131__________________________________________176\n_____________\|____________________________________________\|\n5'-UCA...UACGA________GCCAGUAAU____AUUCUUUAA____A_____U___AUUAU...CAA-3'\n______________CAAAAGUU_________CGUU_________GGCU_UGGUU_UUC\n______________\|\|\|\|\|\|\|\|_________\|\|\|\|_________\|\|\|\|_\|:\|\|\|_\|\|\|\n______________GUUUUCAA_________GCAA_________CCGA_AUCAA_AAG\n3'-CGC...UAGGC________GU________________________A_____U___CUCAA...AAG-5'\n_____________\|____________________________________________\|\n_____________92___________________________________________63\n	133 -- 139	84 -- 90	-16.5622 kcal/mol	8.12255 kcal/mol	2.88465 kcal/mol	131 176@LB@ \| \|@LB@5'-UCA...UACGA GCCAGUAAU AUUCUUUAA A U AUUAU...CAA-3'@LB@ CAAAAGUU CGUU GGCU UGGUU UUC@LB@ \|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\| \|:\|\|\| \|\|\|@LB@ GUUUUCAA GCAA CCGA AUCAA AAG@LB@3'-CGC...UAGGC GU A U CUCAA...AAG-5'@LB@ \| \|@LB@ 92 63@LB@@LB@@LB@Energy -5.56 kcal/mol@LB@Hybridization Energy -16.5622 kcal/mol@LB@Unfolding Energy - mRNA 8.12255 kcal/mol@LB@Unfolding Energy - sRNA 2.88465 kcal/mol@LB@@LB@Position - mRNA 132 -- 175@LB@Position - sRNA 64 -- 91@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 84 -- 90@LB@
132	0.0226	0.5385	b2721	hycE	-8.05	0.224194	140 -- 148	71 -- 79	hydrogenase 3 large subunit	_____________139_______149\n_____________\|_________\|\n5'-UUC...UGGGU_________CAUUU...UGA-3'\n______________UUGGCUUUG\n______________\|\|\|\|\|\|\|\|:\n______________AACCGAAAU\n3'-CGC...AGUGC_________CAAUA...AAG-5'\n_____________\|_________\|\n_____________80________70\n	142 -- 148	71 -- 77	-10.5671 kcal/mol	2.29615 kcal/mol	0.222833 kcal/mol	139 149@LB@ \| \|@LB@5'-UUC...UGGGU CAUUU...UGA-3'@LB@ UUGGCUUUG@LB@ \|\|\|\|\|\|\|\|:@LB@ AACCGAAAU@LB@3'-CGC...AGUGC CAAUA...AAG-5'@LB@ \| \|@LB@ 80 70@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -10.5671 kcal/mol@LB@Unfolding Energy - mRNA 2.29615 kcal/mol@LB@Unfolding Energy - sRNA 0.222833 kcal/mol@LB@@LB@Position - mRNA 140 -- 148@LB@Position - sRNA 71 -- 79@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 71 -- 77@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