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
41	0.008018	0.6129	b1740	nadE	-11.27	0.022577	258 -- 272	38 -- 52	NAD synthetase NH3/glutamine-dependent	_____________257_____________273\n_____________\|_______________\|\n5'-UUC...AUGCU_________A_____CGUAG...ACC-3'\n______________GAAGAGGAA_UUCGU\n______________:\|\|\|\|\|\|\|\|_\|\|\|:\|\n______________UUUCUCCUU_AAGUA\n3'-UUU...GGCAG_________A_____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	260 -- 266	44 -- 50	-15.8385 kcal/mol	3.49717 kcal/mol	1.0693 kcal/mol	257 273@LB@ \| \|@LB@5'-UUC...AUGCU A CGUAG...ACC-3'@LB@ GAAGAGGAA UUCGU@LB@ :\|\|\|\|\|\|\|\| \|\|\|:\|@LB@ UUUCUCCUU AAGUA@LB@3'-UUU...GGCAG A AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -15.8385 kcal/mol@LB@Unfolding Energy - mRNA 3.49717 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 44 -- 50@LB@
42	0.008125	0.6129	b2431	yfeX	-9.88	0.043594	266 -- 278	44 -- 56	porphyrinogen oxidase cytoplasmic	_____________265___________279\n_____________\|_____________\|\n5'-AUU...GCCAA___G_________GUUGA...CCA-3'\n______________CGU_AAAGGGGAA\n______________\|\|\|_\|\|\|\|:\|\|\|\|\n______________GCA_UUUCUCCUU\n3'-UUU...ACCGG___G_________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________57____________43\n	272 -- 278	44 -- 50	-15.4775 kcal/mol	4.65199 kcal/mol	0.948902 kcal/mol	265 279@LB@ \| \|@LB@5'-AUU...GCCAA G GUUGA...CCA-3'@LB@ CGU AAAGGGGAA@LB@ \|\|\| \|\|\|\|:\|\|\|\|@LB@ GCA UUUCUCCUU@LB@3'-UUU...ACCGG G AAAGU...ACA-5'@LB@ \| \|@LB@ 57 43@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -15.4775 kcal/mol@LB@Unfolding Energy - mRNA 4.65199 kcal/mol@LB@Unfolding Energy - sRNA 0.948902 kcal/mol@LB@@LB@Position - mRNA 266 -- 278@LB@Position - sRNA 44 -- 56@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 44 -- 50@LB@
43	0.008509	0.6129	b4322	uxuA	-11.91	0.016653	184 -- 195	44 -- 55	mannonate hydrolase	_____________183__________196\n_____________\|____________\|\n5'-CAU...ACUAU__G_________AAAUC...AUA-3'\n______________GU_AAAGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\|\|\n______________CA_UUUCUCCUU\n3'-UUU...CCGGG__G_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	189 -- 195	44 -- 50	-15.5118 kcal/mol	2.65561 kcal/mol	0.941432 kcal/mol	183 196@LB@ \| \|@LB@5'-CAU...ACUAU G AAAUC...AUA-3'@LB@ GU AAAGAGGAA@LB@ \|\| \|\|\|\|\|\|\|\|\|@LB@ CA UUUCUCCUU@LB@3'-UUU...CCGGG G AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -15.5118 kcal/mol@LB@Unfolding Energy - mRNA 2.65561 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
44	0.008636	0.6129	b3317	rplB	-9.78	0.045660	184 -- 194	43 -- 55	50S ribosomal subunit protein L2	_____________183___________195\n_____________\|_____________\|\n5'-GCA...AGUAA_____________AAUAC...UGC-3'\n______________GUC__GGAGGAGU\n______________\|\|\|__:\|\|\|\|\|:\|\n______________CAG__UCUCCUUA\n3'-UUU...CCGGG___UU________AAGUA...ACA-5'\n_____________\|_____________\|\n_____________56____________42\n	188 -- 194	43 -- 49	-13.3143 kcal/mol	2.58995 kcal/mol	0.946481 kcal/mol	183 195@LB@ \| \|@LB@5'-GCA...AGUAA AAUAC...UGC-3'@LB@ GUC GGAGGAGU@LB@ \|\|\| :\|\|\|\|\|:\|@LB@ CAG UCUCCUUA@LB@3'-UUU...CCGGG UU AAGUA...ACA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -13.3143 kcal/mol@LB@Unfolding Energy - mRNA 2.58995 kcal/mol@LB@Unfolding Energy - sRNA 0.946481 kcal/mol@LB@@LB@Position - mRNA 184 -- 194@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 43 -- 49@LB@
45	0.009176	0.6129	b3389	aroB	-8.88	0.069424	203 -- 218	37 -- 52	3-dehydroquinate synthase	_____________202______________219\n_____________\|________________\|\n5'-ACA...GUUAU________UUG_____ACUCU...CGG-3'\n______________GGAGAGGA___UCGUU\n______________::\|\|\|\|\|\|___\|\|:\|\|\n______________UUUCUCCU___AGUAA\n3'-UUU...GGCAG________UAA_____AAAAA...ACA-5'\n_____________\|________________\|\n_____________53_______________36\n	204 -- 210	45 -- 51	-14.6346 kcal/mol	4.67835 kcal/mol	1.07641 kcal/mol	202 219@LB@ \| \|@LB@5'-ACA...GUUAU UUG ACUCU...CGG-3'@LB@ GGAGAGGA UCGUU@LB@ ::\|\|\|\|\|\| \|\|:\|\|@LB@ UUUCUCCU AGUAA@LB@3'-UUU...GGCAG UAA AAAAA...ACA-5'@LB@ \| \|@LB@ 53 36@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -14.6346 kcal/mol@LB@Unfolding Energy - mRNA 4.67835 kcal/mol@LB@Unfolding Energy - sRNA 1.07641 kcal/mol@LB@@LB@Position - mRNA 203 -- 218@LB@Position - sRNA 37 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 45 -- 51@LB@
46	0.009202	0.6129	b0183	rnhB	-8.44	0.085048	25 -- 32	48 -- 55	ribonuclease HII degrades RNA of DNA-RNA hybrids	_____________24_______33\n_____________\|________\|\n5'-AAU...AGUUA________AUUAU...UCC-3'\n______________GUCAAAGA\n______________\|\|\|\|\|\|\|\|\n______________CAGUUUCU\n3'-UUU...CCGGG________CCUUA...ACA-5'\n_____________\|________\|\n_____________56_______47\n	26 -- 32	48 -- 54	-9.30452 kcal/mol	0.544993 kcal/mol	0.318869 kcal/mol	24 33@LB@ \| \|@LB@5'-AAU...AGUUA AUUAU...UCC-3'@LB@ GUCAAAGA@LB@ \|\|\|\|\|\|\|\|@LB@ CAGUUUCU@LB@3'-UUU...CCGGG CCUUA...ACA-5'@LB@ \| \|@LB@ 56 47@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -9.30452 kcal/mol@LB@Unfolding Energy - mRNA 0.544993 kcal/mol@LB@Unfolding Energy - sRNA 0.318869 kcal/mol@LB@@LB@Position - mRNA 25 -- 32@LB@Position - sRNA 48 -- 55@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 48 -- 54@LB@
47	0.009275	0.6129	b3412	bioH	-9.55	0.050822	229 -- 245	38 -- 55	pimeloyl-ACP methyl ester carboxylesterase	_____________228_________________246\n_____________\|___________________\|\n5'-GGC...CAAAG_____________G_____CUUGU...ACG-3'\n______________GUC__AGGGGAAU_UUCAU\n______________\|\|\|__\|\|:\|\|\|\|\|_\|\|\|\|\|\n______________CAG__UCUCCUUA_AAGUA\n3'-UUU...CCGGG___UU______________AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	233 -- 239	43 -- 49	-15.7204 kcal/mol	5.00086 kcal/mol	1.17036 kcal/mol	228 246@LB@ \| \|@LB@5'-GGC...CAAAG G CUUGU...ACG-3'@LB@ GUC AGGGGAAU UUCAU@LB@ \|\|\| \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ CAG UCUCCUUA AAGUA@LB@3'-UUU...CCGGG UU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -9.55 kcal/mol@LB@Hybridization Energy -15.7204 kcal/mol@LB@Unfolding Energy - mRNA 5.00086 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 229 -- 245@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 43 -- 49@LB@
48	0.00943	0.6129	b3033	yqiB	-8.72	0.074798	113 -- 121	44 -- 52	DUF1249 protein YqiB	_____________112_______122\n_____________\|_________\|\n5'-UGG...GUAGA_________AAUCG...GCG-3'\n______________AGAGGGGAA\n______________\|:\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	115 -- 121	44 -- 50	-10.7393 kcal/mol	1.15971 kcal/mol	0.860683 kcal/mol	112 122@LB@ \| \|@LB@5'-UGG...GUAGA AAUCG...GCG-3'@LB@ AGAGGGGAA@LB@ \|:\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.15971 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 113 -- 121@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 44 -- 50@LB@
49	0.009604	0.6129	b1175	minD	-8.49	0.083180	191 -- 199	40 -- 48	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAACA_________UAUGG...AAA-3'\n______________AGGAAUUUC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCUUAAAG\n3'-UUU...GUUUC_________UAAAA...ACA-5'\n_____________\|_________\|\n_____________49________39\n	193 -- 199	40 -- 46	-11.0161 kcal/mol	1.62901 kcal/mol	0.898161 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAACA UAUGG...AAA-3'@LB@ AGGAAUUUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCUUAAAG@LB@3'-UUU...GUUUC UAAAA...ACA-5'@LB@ \| \|@LB@ 49 39@LB@@LB@@LB@Energy -8.49 kcal/mol@LB@Hybridization Energy -11.0161 kcal/mol@LB@Unfolding Energy - mRNA 1.62901 kcal/mol@LB@Unfolding Energy - sRNA 0.898161 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 40 -- 48@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 40 -- 46@LB@
50	0.009706	0.6129	b0109	nadC	-3.48	0.624399	8 -- 15	22 -- 29	quinolinate phosphoribosyltransferase	_____________7________16\n_____________\|________\|\n____5'-AGGCUAA________ACCAC...AAG-3'\n______________UAUUGUGC\n______________\|\|\|\|:\|\|\|\n______________AUAAUACG\n3'-UUU...AAAUA________GCAGU...ACA-5'\n_____________\|________\|\n_____________30_______21\n	9 -- 15	22 -- 28	-7.42611 kcal/mol	1.02369 kcal/mol	2.92038 kcal/mol	7 16@LB@ \| \|@LB@ 5'-AGGCUAA ACCAC...AAG-3'@LB@ UAUUGUGC@LB@ \|\|\|\|:\|\|\|@LB@ AUAAUACG@LB@3'-UUU...AAAUA GCAGU...ACA-5'@LB@ \| \|@LB@ 30 21@LB@@LB@@LB@Energy -3.48 kcal/mol@LB@Hybridization Energy -7.42611 kcal/mol@LB@Unfolding Energy - mRNA 1.02369 kcal/mol@LB@Unfolding Energy - sRNA 2.92038 kcal/mol@LB@@LB@Position - mRNA 8 -- 15@LB@Position - sRNA 22 -- 29@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 22 -- 28@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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