Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
92	0.004911	0.1855	b3732	atpD	-9.01	0.211333	117 -- 128	1 -- 11	F1 sector of membrane-bound ATP synthase beta subunit	_____________116__________129\n_____________\|____________\|\n5'-GGC...GCUCG_______A____UACUC...AAA-3'\n______________UCAGGCC_GCAU\n______________\|\|\|\|\|\|\|_\|\|\|:\n______________AGUCCGG_CGUG\n3'-UUU...CAAAA____________-5'\n_____________\|___________\|\n_____________12__________1\n	117 -- 123	5 -- 11	-17.8068 kcal/mol	3.15312 kcal/mol	5.60325 kcal/mol	116 129@LB@ \| \|@LB@5'-GGC...GCUCG A UACUC...AAA-3'@LB@ UCAGGCC GCAU@LB@ \|\|\|\|\|\|\| \|\|\|:@LB@ AGUCCGG CGUG@LB@3'-UUU...CAAAA -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -17.8068 kcal/mol@LB@Unfolding Energy - mRNA 3.15312 kcal/mol@LB@Unfolding Energy - sRNA 5.60325 kcal/mol@LB@@LB@Position - mRNA 117 -- 128@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 5 -- 11@LB@
55	0.002731	0.1727	b2480	bcp	-8.89	0.222722	156 -- 187	28 -- 56	peroxiredoxin; thiol peroxidase thioredoxin-dependent	_____________155_________________________________188\n_____________\|___________________________________\|\n5'-GAG...AUUAA______C_______CCCAAC_______________AUGGA...UUC-3'\n______________CGUCGU_AAUUAUU______AUGAUGA___ACAGG\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|______\|\|\|\|\|\|\|___\|\|\|:\|\n______________GCGGCA_UUAAUAA______UACUACU___UGUUC\n3'-UUU...CCGAC______U____________________CAA_____CCGUG...GUG-5'\n_____________\|___________________________________\|\n_____________57__________________________________27\n	176 -- 182	36 -- 42	-21.7802 kcal/mol	6.3273 kcal/mol	6.56571 kcal/mol	155 188@LB@ \| \|@LB@5'-GAG...AUUAA C CCCAAC AUGGA...UUC-3'@LB@ CGUCGU AAUUAUU AUGAUGA ACAGG@LB@ \|\|:\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|:\|@LB@ GCGGCA UUAAUAA UACUACU UGUUC@LB@3'-UUU...CCGAC U CAA CCGUG...GUG-5'@LB@ \| \|@LB@ 57 27@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -21.7802 kcal/mol@LB@Unfolding Energy - mRNA 6.3273 kcal/mol@LB@Unfolding Energy - sRNA 6.56571 kcal/mol@LB@@LB@Position - mRNA 156 -- 187@LB@Position - sRNA 28 -- 56@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 36 -- 42@LB@
139	0.008022	0.2031	b0311	betA	-9.91	0.144745	36 -- 54	64 -- 80	choline dehydrogenase a flavoprotein	_____________35__________________55\n_____________\|___________________\|\n5'-CGU...CUGGA________U____C_____CCCGG...AAG-3'\n______________UCAACACC_GGGG_GAAUC\n______________:\|\|\|\|\|\|\|_:\|\|\|_:\|\|\|\|\n______________GGUUGUGG_UCCC_UUUAG\n3'-UUU...GACGC___________________AACCG...GUG-5'\n_____________\|___________________\|\n_____________81__________________63\n	37 -- 43	73 -- 79	-20.9821 kcal/mol	4.03056 kcal/mol	7.04361 kcal/mol	35 55@LB@ \| \|@LB@5'-CGU...CUGGA U C CCCGG...AAG-3'@LB@ UCAACACC GGGG GAAUC@LB@ :\|\|\|\|\|\|\| :\|\|\| :\|\|\|\|@LB@ GGUUGUGG UCCC UUUAG@LB@3'-UUU...GACGC AACCG...GUG-5'@LB@ \| \|@LB@ 81 63@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -20.9821 kcal/mol@LB@Unfolding Energy - mRNA 4.03056 kcal/mol@LB@Unfolding Energy - sRNA 7.04361 kcal/mol@LB@@LB@Position - mRNA 36 -- 54@LB@Position - sRNA 64 -- 80@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 73 -- 79@LB@
182	0.01083	0.2089	b0314	betT	-9.44	0.176432	217 -- 228	66 -- 77	choline transporter of high affinity	_____________216__________229\n_____________\|____________\|\n5'-UUC...UUCAC___G________AGGAC...UCC-3'\n______________ACA_CAGGGAAA\n______________\|\|\|_\|\|\|\|\|\|\|\|\n______________UGU_GUCCCUUU\n3'-UUU...GCGGU___G________AGAAC...GUG-5'\n_____________\|____________\|\n_____________78___________65\n	222 -- 228	66 -- 72	-15.8835 kcal/mol	1.82432 kcal/mol	4.61119 kcal/mol	216 229@LB@ \| \|@LB@5'-UUC...UUCAC G AGGAC...UCC-3'@LB@ ACA CAGGGAAA@LB@ \|\|\| \|\|\|\|\|\|\|\|@LB@ UGU GUCCCUUU@LB@3'-UUU...GCGGU G AGAAC...GUG-5'@LB@ \| \|@LB@ 78 65@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -15.8835 kcal/mol@LB@Unfolding Energy - mRNA 1.82432 kcal/mol@LB@Unfolding Energy - sRNA 4.61119 kcal/mol@LB@@LB@Position - mRNA 217 -- 228@LB@Position - sRNA 66 -- 77@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 66 -- 72@LB@
141	0.008132	0.2031	b3412	bioH	-10.51	0.111302	230 -- 255	56 -- 74	pimeloyl-ACP methyl ester carboxylesterase	_____________229________________________256\n_____________\|__________________________\|\n5'-GGC...AAAGG________AUGUUC______U_____UGCAC...ACG-3'\n______________UCAGGGGA______AUCUUG_GCUGC\n______________:\|\|\|\|\|:\|______\|\|\|\|\|\|_\|\|\|\|\|\n______________GGUCCCUU______UAGAAC_CGACG\n3'-UUU...GUUGU__________________________CGGCA...GUG-5'\n_____________\|__________________________\|\n_____________75_________________________55\n	231 -- 237	67 -- 73	-25.2186 kcal/mol	6.56983 kcal/mol	8.13729 kcal/mol	229 256@LB@ \| \|@LB@5'-GGC...AAAGG AUGUUC U UGCAC...ACG-3'@LB@ UCAGGGGA AUCUUG GCUGC@LB@ :\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\|\|@LB@ GGUCCCUU UAGAAC CGACG@LB@3'-UUU...GUUGU CGGCA...GUG-5'@LB@ \| \|@LB@ 75 55@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -25.2186 kcal/mol@LB@Unfolding Energy - mRNA 6.56983 kcal/mol@LB@Unfolding Energy - sRNA 8.13729 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 56 -- 74@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 67 -- 73@LB@
48	0.002388	0.1727	b2198	ccmD	-12.59	0.043972	250 -- 282	36 -- 77	cytochrome c biogenesis protein; heme export ABC transporter holo-CcmE release factor	_____________249________________________________________283\n_____________\|__________________________________________\|\n5'-UGG...CGGUU_____UUUUUU_____________G_________________CCGUU...UGG-3'\n______________ACGCC______GUC_UGGCUG_GC_GUG_______GUGAUGA\n______________\|\|:\|\|______:\|\|_\|\|\|\|\|\|_\|\|_\|\|:_______:\|\|\|\|\|\|\n______________UGUGG______UAG_ACCGAC_CG_CAU_______UACUACU\n3'-UUU...GCGGU_____UCCCUU___A______G__G___UUAAUAA_______CAAUG...GUG-5'\n_____________\|__________________________________________\|\n_____________78_________________________________________35\n	276 -- 282	36 -- 42	-31.2682 kcal/mol	9.31707 kcal/mol	9.36195 kcal/mol	249 283@LB@ \| \|@LB@5'-UGG...CGGUU UUUUUU G CCGUU...UGG-3'@LB@ ACGCC GUC UGGCUG GC GUG GUGAUGA@LB@ \|\|:\|\| :\|\| \|\|\|\|\|\| \|\| \|\|: :\|\|\|\|\|\|@LB@ UGUGG UAG ACCGAC CG CAU UACUACU@LB@3'-UUU...GCGGU UCCCUU A G G UUAAUAA CAAUG...GUG-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -31.2682 kcal/mol@LB@Unfolding Energy - mRNA 9.31707 kcal/mol@LB@Unfolding Energy - sRNA 9.36195 kcal/mol@LB@@LB@Position - mRNA 250 -- 282@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 36 -- 42@LB@
37	0.002023	0.1727	b2197	ccmE	-14.61	0.017549	166 -- 218	48 -- 94	periplasmic heme chaperone	_____________165___________________________________________________________219\n_____________\|_____________________________________________________________\|\n5'-CCU...GUGAG_____UUUAC______________G____A_____________AUGAAUAUUC________AACCG...AUA-3'\n______________GCGCG_____GUGCUGCG_CAACA_CAGG________GGCUGC__________GCCGUAAA\n______________\|\|\|\|\|_____:\|:\|\|\|\|\|_\|\|\|\|\|_\|\|\|\|________\|\|\|\|\|\|__________\|\|\|\|\|\|\|\|\n______________CGCGC_____UAUGACGC_GUUGU_GUCC________CCGACG__________CGGCAUUU\n3'-UUU...CCCCA_____U____________G_____G____CUUUAGAA________________________AAUAA...GUG-5'\n_____________\|_____________________________________________________________\|\n_____________95____________________________________________________________47\n	212 -- 218	48 -- 54	-51.9512 kcal/mol	20.0441 kcal/mol	17.2978 kcal/mol	165 219@LB@ \| \|@LB@5'-CCU...GUGAG UUUAC G A AUGAAUAUUC AACCG...AUA-3'@LB@ GCGCG GUGCUGCG CAACA CAGG GGCUGC GCCGUAAA@LB@ \|\|\|\|\| :\|:\|\|\|\|\| \|\|\|\|\| \|\|\|\| \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CGCGC UAUGACGC GUUGU GUCC CCGACG CGGCAUUU@LB@3'-UUU...CCCCA U G G CUUUAGAA AAUAA...GUG-5'@LB@ \| \|@LB@ 95 47@LB@@LB@@LB@Energy -14.61 kcal/mol@LB@Hybridization Energy -51.9512 kcal/mol@LB@Unfolding Energy - mRNA 20.0441 kcal/mol@LB@Unfolding Energy - sRNA 17.2978 kcal/mol@LB@@LB@Position - mRNA 166 -- 218@LB@Position - sRNA 48 -- 94@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 48 -- 54@LB@
133	0.007533	0.1993	b2194	ccmH	-11.64	0.067570	191 -- 199	1 -- 9	heme lyase CcmH subunit	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAAGG_________AAUGA...AGU-3'\n______________AGGCCGCAC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCGGCGUG\n3'-UUU...AAAAG_________-5'\n_____________\|________\|\n_____________10_______1\n	193 -- 199	1 -- 7	-19.8862 kcal/mol	2.96679 kcal/mol	5.10726 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAAGG AAUGA...AGU-3'@LB@ AGGCCGCAC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCGGCGUG@LB@3'-UUU...AAAAG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -19.8862 kcal/mol@LB@Unfolding Energy - mRNA 2.96679 kcal/mol@LB@Unfolding Energy - sRNA 5.10726 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 1 -- 7@LB@
31	0.001682	0.1727	b1887	cheW	-12.93	0.037697	13 -- 28	70 -- 86	purine-binding chemotaxis protein	_____________12________________29\n_____________\|_________________\|\n5'-GUG...AAUUA_________________UUGUG...UCC-3'\n______________AUUG_GUCAACACCAGG\n______________\|:\|\|_\|:\|\|\|\|\|\|\|\|\|\|\n______________UGAC_CGGUUGUGGUCC\n3'-UUU...GCUUA____G____________CUUUA...GUG-5'\n_____________\|_________________\|\n_____________87________________69\n	22 -- 28	70 -- 76	-24.746 kcal/mol	4.53921 kcal/mol	7.27772 kcal/mol	12 29@LB@ \| \|@LB@5'-GUG...AAUUA UUGUG...UCC-3'@LB@ AUUG GUCAACACCAGG@LB@ \|:\|\| \|:\|\|\|\|\|\|\|\|\|\|@LB@ UGAC CGGUUGUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -24.746 kcal/mol@LB@Unfolding Energy - mRNA 4.53921 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 13 -- 28@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 70 -- 76@LB@
123	0.00672	0.1913	b0882	clpA	-10.14	0.130927	50 -- 58	66 -- 74	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity	_____________49________59\n_____________\|_________\|\n5'-UUU...CACUA_________GGCCA...CGC-3'\n______________CCAGGGGAA\n______________\|\|\|\|\|\|:\|\|\n______________GGUCCCUUU\n3'-UUU...GUUGU_________AGAAC...GUG-5'\n_____________\|_________\|\n_____________75________65\n	52 -- 58	66 -- 72	-13.8898 kcal/mol	0.70189 kcal/mol	3.04768 kcal/mol	49 59@LB@ \| \|@LB@5'-UUU...CACUA GGCCA...CGC-3'@LB@ CCAGGGGAA@LB@ \|\|\|\|\|\|:\|\|@LB@ GGUCCCUUU@LB@3'-UUU...GUUGU AGAAC...GUG-5'@LB@ \| \|@LB@ 75 65@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -13.8898 kcal/mol@LB@Unfolding Energy - mRNA 0.70189 kcal/mol@LB@Unfolding Energy - sRNA 3.04768 kcal/mol@LB@@LB@Position - mRNA 50 -- 58@LB@Position - sRNA 66 -- 74@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 66 -- 72@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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