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
99	0.01653	0.5385	b0004	thrC	-7.16	0.308279	183 -- 210	49 -- 64	L-threonine synthase	_____________182__________________________211\n_____________\|____________________________\|\n5'-CGC...GCGCA_____AC___AAAACUAAAU________ACAAU...ACG-3'\n______________CGAGU__UGG__________GAAACUCU\n______________\|\|\|\|\|__\|\|:__________\|\|\|\|\|\|\|\|\n______________GCUCA__ACU__________CUUUGAGA\n3'-CGC...AAUAA____________________________GCUUU...AAG-5'\n_____________\|____________________________\|\n_____________65___________________________48\n	204 -- 210	49 -- 55	-14.0058 kcal/mol	2.63666 kcal/mol	4.20534 kcal/mol	182 211@LB@ \| \|@LB@5'-CGC...GCGCA AC AAAACUAAAU ACAAU...ACG-3'@LB@ CGAGU UGG GAAACUCU@LB@ \|\|\|\|\| \|\|: \|\|\|\|\|\|\|\|@LB@ GCUCA ACU CUUUGAGA@LB@3'-CGC...AAUAA GCUUU...AAG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -14.0058 kcal/mol@LB@Unfolding Energy - mRNA 2.63666 kcal/mol@LB@Unfolding Energy - sRNA 4.20534 kcal/mol@LB@@LB@Position - mRNA 183 -- 210@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 49 -- 55@LB@
59	0.01163	0.5385	b1279	yciS	-7.12	0.313424	44 -- 60	74 -- 90	DUF1049 family inner membrane protein function unknown	_____________43________________61\n_____________\|_________________\|\n5'-ACC...AACAA_______A___C_____GAUUU...UGU-3'\n______________GAAAGUU_ACG_UGGUU\n______________:\|\|\|\|\|\|_\|\|\|_\|\|\|:\|\n______________UUUUCAA_UGC_ACCGA\n3'-CGC...AGGCG_______G___A_____AAUCA...AAG-5'\n_____________\|_________________\|\n_____________91________________73\n	44 -- 50	84 -- 90	-13.3715 kcal/mol	5.7376 kcal/mol	0.517587 kcal/mol	43 61@LB@ \| \|@LB@5'-ACC...AACAA A C GAUUU...UGU-3'@LB@ GAAAGUU ACG UGGUU@LB@ :\|\|\|\|\|\| \|\|\| \|\|\|:\|@LB@ UUUUCAA UGC ACCGA@LB@3'-CGC...AGGCG G A AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -7.12 kcal/mol@LB@Hybridization Energy -13.3715 kcal/mol@LB@Unfolding Energy - mRNA 5.7376 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 44 -- 60@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 84 -- 90@LB@
188	0.03339	0.5559	b3232	zapE	-6.91	0.336884	267 -- 282	15 -- 35	divisome ATPase	_____________266____________________283\n_____________\|______________________\|\n5'-AGG...CCGAC___G__________________CCGUC...AAA-3'\n______________GAC_UUCA______AAAAGAGG\n______________\|\|\|_\|\|\|\|______\|\|\|\|\|\|\|\|\n______________CUG_AAGU______UUUUCUCC\n3'-CGC...CGUCA________UCCCAA________ACGGC...AAG-5'\n_____________\|______________________\|\n_____________36_____________________14\n	276 -- 282	15 -- 21	-13.3674 kcal/mol	3.12995 kcal/mol	3.33058 kcal/mol	266 283@LB@ \| \|@LB@5'-AGG...CCGAC G CCGUC...AAA-3'@LB@ GAC UUCA AAAAGAGG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUG AAGU UUUUCUCC@LB@3'-CGC...CGUCA UCCCAA ACGGC...AAG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -13.3674 kcal/mol@LB@Unfolding Energy - mRNA 3.12995 kcal/mol@LB@Unfolding Energy - sRNA 3.33058 kcal/mol@LB@@LB@Position - mRNA 267 -- 282@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 15 -- 21@LB@
133	0.02275	0.5385	b0177	bamA	-6.79	0.350358	265 -- 271	23 -- 29	BamABCDE complex OM biogenesis outer membrane pore-forming assembly factor	_____________264_____272\n_____________\|_______\|\n5'-CUG...UGCUG_______CGUAG...GCC-3'\n______________AAGGGUU\n______________\|\|\|\|\|\|\|\n______________UUCCCAA\n3'-CGC...UGAAG_______UUUUC...AAG-5'\n_____________\|_______\|\n_____________30______22\n	265 -- 271	23 -- 29	-7.93739 kcal/mol	1.09969 kcal/mol	0.0462613 kcal/mol	264 272@LB@ \| \|@LB@5'-CUG...UGCUG CGUAG...GCC-3'@LB@ AAGGGUU@LB@ \|\|\|\|\|\|\|@LB@ UUCCCAA@LB@3'-CGC...UGAAG UUUUC...AAG-5'@LB@ \| \|@LB@ 30 22@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -7.93739 kcal/mol@LB@Unfolding Energy - mRNA 1.09969 kcal/mol@LB@Unfolding Energy - sRNA 0.0462613 kcal/mol@LB@@LB@Position - mRNA 265 -- 271@LB@Position - sRNA 23 -- 29@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 23 -- 29@LB@
105	0.01788	0.5385	b0619	citA	-6.78	0.351941	4 -- 24	64 -- 89	sensory histidine kinase in two-component regulatory system with CitB	_____________3__________________________25\n_____________\|__________________________\|\n________5'-CAU______AG__________________AUUUA...UCA-3'\n______________AGAGUU_____UGGUUUU__UUAUUU\n______________\|:\|\|\|\|_____\|\|\|:\|\|\|__\|\|\|\|\|:\n______________UUUCAA_____ACCGAAA__AAUAAG\n3'-CGC...GGCGU______GUGCA_______UC______CUCAA...AAG-5'\n_____________\|__________________________\|\n_____________90_________________________63\n	12 -- 18	72 -- 78	-10.9037 kcal/mol	3.54899 kcal/mol	0.576654 kcal/mol	3 25@LB@ \| \|@LB@ 5'-CAU AG AUUUA...UCA-3'@LB@ AGAGUU UGGUUUU UUAUUU@LB@ \|:\|\|\|\| \|\|\|:\|\|\| \|\|\|\|\|:@LB@ UUUCAA ACCGAAA AAUAAG@LB@3'-CGC...GGCGU GUGCA UC CUCAA...AAG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -10.9037 kcal/mol@LB@Unfolding Energy - mRNA 3.54899 kcal/mol@LB@Unfolding Energy - sRNA 0.576654 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 12 -- 18@LB@Position Seed - sRNA 72 -- 78@LB@
190	0.03345	0.5559	b4090	rpiB	-6.75	0.355761	259 -- 286	57 -- 78	ribose 5-phosphate isomerase B/allose 6-phosphate isomerase	_____________258__________________________287\n_____________\|____________________________\|\n5'-AAC...AAUAG____ACA________AGCG___C_____AGUGA...AAG-3'\n______________UGGC___UUUAGUUG____UGG_GUUGA\n______________\|\|\|\|___\|\|\|\|\|\|\|:____:\|:_\|\|\|\|\|\n______________ACCG___AAAUCAAU____GCU_CAACU\n3'-CGC...GUGCA_______________AA___________CUUUG...AAG-5'\n_____________\|____________________________\|\n_____________79___________________________56\n	267 -- 273	67 -- 73	-15.2709 kcal/mol	7.30632 kcal/mol	1.21856 kcal/mol	258 287@LB@ \| \|@LB@5'-AAC...AAUAG ACA AGCG C AGUGA...AAG-3'@LB@ UGGC UUUAGUUG UGG GUUGA@LB@ \|\|\|\| \|\|\|\|\|\|\|: :\|: \|\|\|\|\|@LB@ ACCG AAAUCAAU GCU CAACU@LB@3'-CGC...GUGCA AA CUUUG...AAG-5'@LB@ \| \|@LB@ 79 56@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -15.2709 kcal/mol@LB@Unfolding Energy - mRNA 7.30632 kcal/mol@LB@Unfolding Energy - sRNA 1.21856 kcal/mol@LB@@LB@Position - mRNA 259 -- 286@LB@Position - sRNA 57 -- 78@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 67 -- 73@LB@
83	0.01501	0.5385	b2114	metG	-6.55	0.379655	47 -- 64	63 -- 79	methionyl-tRNA synthetase	_____________46_________________65\n_____________\|__________________\|\n5'-AUU...GUGAU_____CUG__A_______UUCAU...AUG-3'\n______________UUGGC___GG_UUGUUCG\n______________\|\|\|\|\|___:\|_\|\|:\|\|\|\|\n______________AACCG___UC_AAUAAGC\n3'-CGC...AGUGC_____AAA__________UCAAC...AAG-5'\n_____________\|__________________\|\n_____________80_________________62\n	58 -- 64	63 -- 69	-14.0866 kcal/mol	6.80006 kcal/mol	0.735636 kcal/mol	46 65@LB@ \| \|@LB@5'-AUU...GUGAU CUG A UUCAU...AUG-3'@LB@ UUGGC GG UUGUUCG@LB@ \|\|\|\|\| :\| \|\|:\|\|\|\|@LB@ AACCG UC AAUAAGC@LB@3'-CGC...AGUGC AAA UCAAC...AAG-5'@LB@ \| \|@LB@ 80 62@LB@@LB@@LB@Energy -6.55 kcal/mol@LB@Hybridization Energy -14.0866 kcal/mol@LB@Unfolding Energy - mRNA 6.80006 kcal/mol@LB@Unfolding Energy - sRNA 0.735636 kcal/mol@LB@@LB@Position - mRNA 47 -- 64@LB@Position - sRNA 63 -- 79@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 63 -- 69@LB@
79	0.01412	0.5385	b2830	rppH	-5.99	0.454649	93 -- 100	64 -- 71	RNA pyrophosphohydrolase	_____________92_______101\n_____________\|________\|\n5'-UUC...CUGUG________AAUUG...GGC-3'\n______________AGUUAUUC\n______________\|\|\|\|\|\|\|\|\n______________UCAAUAAG\n3'-CGC...CGAAA________CUCAA...AAG-5'\n_____________\|________\|\n_____________72_______63\n	94 -- 100	64 -- 70	-7.84269 kcal/mol	1.74359 kcal/mol	0.11296 kcal/mol	92 101@LB@ \| \|@LB@5'-UUC...CUGUG AAUUG...GGC-3'@LB@ AGUUAUUC@LB@ \|\|\|\|\|\|\|\|@LB@ UCAAUAAG@LB@3'-CGC...CGAAA CUCAA...AAG-5'@LB@ \| \|@LB@ 72 63@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -7.84269 kcal/mol@LB@Unfolding Energy - mRNA 1.74359 kcal/mol@LB@Unfolding Energy - sRNA 0.11296 kcal/mol@LB@@LB@Position - mRNA 93 -- 100@LB@Position - sRNA 64 -- 71@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 64 -- 70@LB@
163	0.02879	0.5559	b4244	pyrI	-5.82	0.477897	276 -- 293	60 -- 77	aspartate carbamoyltransferase regulatory subunit	_____________275________________294\n_____________\|__________________\|\n5'-UUC...AGAUC_______AGCUG______CUGUUCA-3'\n______________GGUUUUA_____UUGAGU\n______________\|\|:\|\|\|\|_____\|:\|\|\|\|\n______________CCGAAAU_____AGCUCA\n3'-CGC...UGCAA_______CAAUA______ACUCU...AAG-5'\n_____________\|__________________\|\n_____________78_________________59\n	276 -- 282	71 -- 77	-12.7499 kcal/mol	6.13118 kcal/mol	0.796465 kcal/mol	275 294@LB@ \| \|@LB@5'-UUC...AGAUC AGCUG CUGUUCA-3'@LB@ GGUUUUA UUGAGU@LB@ \|\|:\|\|\|\| \|:\|\|\|\|@LB@ CCGAAAU AGCUCA@LB@3'-CGC...UGCAA CAAUA ACUCU...AAG-5'@LB@ \| \|@LB@ 78 59@LB@@LB@@LB@Energy -5.82 kcal/mol@LB@Hybridization Energy -12.7499 kcal/mol@LB@Unfolding Energy - mRNA 6.13118 kcal/mol@LB@Unfolding Energy - sRNA 0.796465 kcal/mol@LB@@LB@Position - mRNA 276 -- 293@LB@Position - sRNA 60 -- 77@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 71 -- 77@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@

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)

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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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