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
164	0.03346	0.6177	b1449	curA	-5.87	0.264423	114 -- 122	45 -- 53	curcumin/dihydrocurcumin reductase NADPH-dependent	_____________113_______123\n_____________\|_________\|\n5'-CGG...UGUUG_________UGUGA...UCG-3'\n______________CAGAGGGGA\n______________\|\|:\|\|:\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	116 -- 122	45 -- 51	-11.6619 kcal/mol	4.87234 kcal/mol	0.917553 kcal/mol	113 123@LB@ \| \|@LB@5'-CGG...UGUUG UGUGA...UCG-3'@LB@ CAGAGGGGA@LB@ \|\|:\|\|:\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -5.87 kcal/mol@LB@Hybridization Energy -11.6619 kcal/mol@LB@Unfolding Energy - mRNA 4.87234 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 114 -- 122@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 116 -- 122@LB@Position Seed - sRNA 45 -- 51@LB@
112	0.02248	0.6177	b2796	sdaC	-8.62	0.078257	115 -- 131	34 -- 50	putative serine transporter	_____________114_______________132\n_____________\|_________________\|\n5'-AUC...CCGAU___CA____________ACGGU...CAA-3'\n______________AGA__GAUUUCAUUUUU\n______________\|\|\|__:\|\|\|\|\|\|\|\|\|\|\|\n______________UCU__UUAAAGUAAAAA\n3'-UUU...CAGUU___CC____________AAUAA...ACA-5'\n_____________\|_________________\|\n_____________51________________33\n	125 -- 131	34 -- 40	-11.667 kcal/mol	1.97198 kcal/mol	1.0739 kcal/mol	114 132@LB@ \| \|@LB@5'-AUC...CCGAU CA ACGGU...CAA-3'@LB@ AGA GAUUUCAUUUUU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\|\|\|@LB@ UCU UUAAAGUAAAAA@LB@3'-UUU...CAGUU CC AAUAA...ACA-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -11.667 kcal/mol@LB@Unfolding Energy - mRNA 1.97198 kcal/mol@LB@Unfolding Energy - sRNA 1.0739 kcal/mol@LB@@LB@Position - mRNA 115 -- 131@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 34 -- 40@LB@
117	0.02321	0.6177	b1712	ihfA	-8.91	0.068436	115 -- 126	45 -- 56	integration host factor (IHF) DNA-binding protein alpha subunit	_____________114__________127\n_____________\|____________\|\n5'-CGU...ACACU__AA________GAUUG...AGA-3'\n______________CG__GAAGAGGA\n______________\|\|__:\|\|\|\|\|\|\|\n______________GC__UUUCUCCU\n3'-UUU...ACCGG__AG________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	120 -- 126	45 -- 51	-12.2887 kcal/mol	2.43966 kcal/mol	0.938337 kcal/mol	114 127@LB@ \| \|@LB@5'-CGU...ACACU AA GAUUG...AGA-3'@LB@ CG GAAGAGGA@LB@ \|\| :\|\|\|\|\|\|\|@LB@ GC UUUCUCCU@LB@3'-UUU...ACCGG AG UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -12.2887 kcal/mol@LB@Unfolding Energy - mRNA 2.43966 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 115 -- 126@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 45 -- 51@LB@
69	0.01434	0.6177	b0551	quuD	-6.03	0.248082	117 -- 124	48 -- 55	DLP12 prophage; putative antitermination protein	_____________116______125\n_____________\|________\|\n5'-ACU...AUGAA________UAACA...GAU-3'\n______________GUCAGAGA\n______________\|\|\|\|:\|\|\|\n______________CAGUUUCU\n3'-UUU...CCGGG________CCUUA...ACA-5'\n_____________\|________\|\n_____________56_______47\n	118 -- 124	48 -- 54	-9.27195 kcal/mol	2.92769 kcal/mol	0.318869 kcal/mol	116 125@LB@ \| \|@LB@5'-ACU...AUGAA UAACA...GAU-3'@LB@ GUCAGAGA@LB@ \|\|\|\|:\|\|\|@LB@ CAGUUUCU@LB@3'-UUU...CCGGG CCUUA...ACA-5'@LB@ \| \|@LB@ 56 47@LB@@LB@@LB@Energy -6.03 kcal/mol@LB@Hybridization Energy -9.27195 kcal/mol@LB@Unfolding Energy - mRNA 2.92769 kcal/mol@LB@Unfolding Energy - sRNA 0.318869 kcal/mol@LB@@LB@Position - mRNA 117 -- 124@LB@Position - sRNA 48 -- 55@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 48 -- 54@LB@
33	0.006504	0.6129	b1937	fliE	-6.45	0.207626	119 -- 135	24 -- 40	flagellar basal-body component	_____________118_______________136\n_____________\|_________________\|\n5'-CUG...AAACC_____________C___UUAGC...GUU-3'\n______________CGUUUUUUUGUUG_UAU\n______________\|:\|\|\|\|\|\|\|:\|\|:_\|\|\|\n______________GUAAAAAAAUAAU_AUA\n3'-UUU...UUAAA_____________A___CGGCA...ACA-5'\n_____________\|_________________\|\n_____________41________________23\n	124 -- 130	29 -- 35	-10.2961 kcal/mol	2.85244 kcal/mol	0.998368 kcal/mol	118 136@LB@ \| \|@LB@5'-CUG...AAACC C UUAGC...GUU-3'@LB@ CGUUUUUUUGUUG UAU@LB@ \|:\|\|\|\|\|\|\|:\|\|: \|\|\|@LB@ GUAAAAAAAUAAU AUA@LB@3'-UUU...UUAAA A CGGCA...ACA-5'@LB@ \| \|@LB@ 41 23@LB@@LB@@LB@Energy -6.45 kcal/mol@LB@Hybridization Energy -10.2961 kcal/mol@LB@Unfolding Energy - mRNA 2.85244 kcal/mol@LB@Unfolding Energy - sRNA 0.998368 kcal/mol@LB@@LB@Position - mRNA 119 -- 135@LB@Position - sRNA 24 -- 40@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 29 -- 35@LB@
86	0.01794	0.6177	b3260	dusB	-7.53	0.128932	119 -- 138	38 -- 55	tRNA-dihydrouridine synthase B	_____________118__________________139\n_____________\|____________________\|\n5'-ACU...GAUUG_______UUU__CC______CUCGU...GAG-3'\n______________GUCAAAG___GG__UUUCAU\n______________\|\|\|\|\|\|\|___\|\|__\|\|\|\|\|\|\n______________CAGUUUC___CC__AAAGUA\n3'-UUU...CCGGG_______U____UU______AAAAA...ACA-5'\n_____________\|____________________\|\n_____________56___________________37\n	119 -- 125	49 -- 55	-13.3869 kcal/mol	4.6894 kcal/mol	1.17036 kcal/mol	118 139@LB@ \| \|@LB@5'-ACU...GAUUG UUU CC CUCGU...GAG-3'@LB@ GUCAAAG GG UUUCAU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ CAGUUUC CC AAAGUA@LB@3'-UUU...CCGGG U UU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -13.3869 kcal/mol@LB@Unfolding Energy - mRNA 4.6894 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 119 -- 138@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 49 -- 55@LB@
85	0.01786	0.6177	b1427	rimL	-14.01	0.006161	123 -- 133	46 -- 56	ribosomal-protein-L7/L12-serine acetyltransferase	_____________122_________134\n_____________\|___________\|\n5'-GAU...GAGAG___________UGUAA...CCU-3'\n______________CGUCAAAGAGG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCUCC\n3'-UUU...ACCGG___________UUAAA...ACA-5'\n_____________\|___________\|\n_____________57__________45\n	127 -- 133	46 -- 52	-17.3934 kcal/mol	2.45026 kcal/mol	0.93204 kcal/mol	122 134@LB@ \| \|@LB@5'-GAU...GAGAG UGUAA...CCU-3'@LB@ CGUCAAAGAGG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCUCC@LB@3'-UUU...ACCGG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -17.3934 kcal/mol@LB@Unfolding Energy - mRNA 2.45026 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 123 -- 133@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 46 -- 52@LB@
89	0.01853	0.6177	b1448	mnaT	-8.57	0.080000	123 -- 134	43 -- 54	methionine N-acyltransferase; L-amino acid N-acyltransferase	_____________122__________135\n_____________\|____________\|\n5'-CGC...UAAUU___UC_______CCGUU...CGG-3'\n______________UCA__GAGGAAU\n______________\|\|\|__\|\|\|\|\|\|\|\n______________AGU__CUCCUUA\n3'-UUU...CGGGC___UU_______AAGUA...ACA-5'\n_____________\|____________\|\n_____________55___________42\n	128 -- 134	43 -- 49	-11.9422 kcal/mol	2.42412 kcal/mol	0.944705 kcal/mol	122 135@LB@ \| \|@LB@5'-CGC...UAAUU UC CCGUU...CGG-3'@LB@ UCA GAGGAAU@LB@ \|\|\| \|\|\|\|\|\|\|@LB@ AGU CUCCUUA@LB@3'-UUU...CGGGC UU AAGUA...ACA-5'@LB@ \| \|@LB@ 55 42@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -11.9422 kcal/mol@LB@Unfolding Energy - mRNA 2.42412 kcal/mol@LB@Unfolding Energy - sRNA 0.944705 kcal/mol@LB@@LB@Position - mRNA 123 -- 134@LB@Position - sRNA 43 -- 54@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 43 -- 49@LB@
129	0.02539	0.6177	b0129	yadI	-10.21	0.037333	124 -- 136	40 -- 52	putative PTS Enzyme IIA	_____________123___________137\n_____________\|_____________\|\n5'-CUG...UUGGG_____________GACGG...UGA-3'\n______________GGAGAGGAGUUUU\n______________::\|\|\|\|\|\|:\|\|\|:\n______________UUUCUCCUUAAAG\n3'-UUU...GGCAG_____________UAAAA...ACA-5'\n_____________\|_____________\|\n_____________53____________39\n	130 -- 136	40 -- 46	-14.8894 kcal/mol	3.74683 kcal/mol	0.936082 kcal/mol	123 137@LB@ \| \|@LB@5'-CUG...UUGGG GACGG...UGA-3'@LB@ GGAGAGGAGUUUU@LB@ ::\|\|\|\|\|\|:\|\|\|:@LB@ UUUCUCCUUAAAG@LB@3'-UUU...GGCAG UAAAA...ACA-5'@LB@ \| \|@LB@ 53 39@LB@@LB@@LB@Energy -10.21 kcal/mol@LB@Hybridization Energy -14.8894 kcal/mol@LB@Unfolding Energy - mRNA 3.74683 kcal/mol@LB@Unfolding Energy - sRNA 0.936082 kcal/mol@LB@@LB@Position - mRNA 124 -- 136@LB@Position - sRNA 40 -- 52@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 40 -- 46@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@

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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