Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
191	0.01886	0.3104	b3494	uspB	-6.32	0.440313	280 -- 286	5 -- 11	universal stress (ethanol tolerance) protein B	_____________279_____287\n_____________\|_______\|\n5'-AAU...ACUAC_______GUUAG...UGC-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	280 -- 286	5 -- 11	-11.0709 kcal/mol	3.63469 kcal/mol	1.11145 kcal/mol	279 287@LB@ \| \|@LB@5'-AAU...ACUAC GUUAG...UGC-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -11.0709 kcal/mol@LB@Unfolding Energy - mRNA 3.63469 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 280 -- 286@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 5 -- 11@LB@
192	0.01895	0.3104	b3333	gspL	-4.89	0.645256	110 -- 132	1 -- 21	general secretory pathway component cryptic	_____________109______________________133\n_____________\|________________________\|\n5'-GAU...CCAGG____________CAUAUU______AACCG...CGC-3'\n______________GAUGGCAAA_GC______UUUUUC\n______________\|\|\|::\|\|\|\|_\|\|______\|:\|\|\|\|\n______________CUAUUGUUU_CG______AGAAAG\n3'-UUU...UACUA_________A__CGC_________-5'\n_____________\|_______________________\|\n_____________22______________________1\n	110 -- 116	15 -- 21	-12.6455 kcal/mol	6.50221 kcal/mol	1.25763 kcal/mol	109 133@LB@ \| \|@LB@5'-GAU...CCAGG CAUAUU AACCG...CGC-3'@LB@ GAUGGCAAA GC UUUUUC@LB@ \|\|\|::\|\|\|\| \|\| \|:\|\|\|\|@LB@ CUAUUGUUU CG AGAAAG@LB@3'-UUU...UACUA A CGC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -4.89 kcal/mol@LB@Hybridization Energy -12.6455 kcal/mol@LB@Unfolding Energy - mRNA 6.50221 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 110 -- 132@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 15 -- 21@LB@
193	0.01896	0.3104	b3181	greA	-10.36	0.105339	194 -- 204	10 -- 20	transcript cleavage factor	_____________193_________205\n_____________\|___________\|\n5'-CGC...GAGGU___________AAGCU...UCG-3'\n______________AUAACAAAUGC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UAUUGUUUACG\n3'-UUU...ACUAC___________CGCAG...AAG-5'\n_____________\|___________\|\n_____________21__________9\n	198 -- 204	10 -- 16	-13.1767 kcal/mol	1.58941 kcal/mol	1.22774 kcal/mol	193 205@LB@ \| \|@LB@5'-CGC...GAGGU AAGCU...UCG-3'@LB@ AUAACAAAUGC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UAUUGUUUACG@LB@3'-UUU...ACUAC CGCAG...AAG-5'@LB@ \| \|@LB@ 21 9@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -13.1767 kcal/mol@LB@Unfolding Energy - mRNA 1.58941 kcal/mol@LB@Unfolding Energy - sRNA 1.22774 kcal/mol@LB@@LB@Position - mRNA 194 -- 204@LB@Position - sRNA 10 -- 20@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 10 -- 16@LB@
194	0.0191	0.3104	b2698	recX	-10.17	0.113250	93 -- 107	8 -- 22	regulatory protein for RecA	_____________92______________108\n_____________\|_______________\|\n5'-AAA...GUAGA__________G____AGCAG...GAC-3'\n______________UGAUAGCGAA_GCGU\n______________\|\|\|\|\|:\|:\|\|_\|\|\|:\n______________ACUAUUGUUU_CGCG\n3'-UUU...CUACU__________A____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	96 -- 102	13 -- 19	-16.2974 kcal/mol	4.88496 kcal/mol	1.23838 kcal/mol	92 108@LB@ \| \|@LB@5'-AAA...GUAGA G AGCAG...GAC-3'@LB@ UGAUAGCGAA GCGU@LB@ \|\|\|\|\|:\|:\|\| \|\|\|:@LB@ ACUAUUGUUU CGCG@LB@3'-UUU...CUACU A CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -16.2974 kcal/mol@LB@Unfolding Energy - mRNA 4.88496 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 93 -- 107@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 13 -- 19@LB@
195	0.01912	0.3104	b3910	yiiM	-10.43	0.102344	196 -- 205	9 -- 18	6-N-hydroxylaminopurine resistance protein	_____________195________206\n_____________\|__________\|\n5'-UAA...GAGGG__________AUAUC...UGC-3'\n______________AACAGAUGCG\n______________\|\|\|\|:\|\|\|\|\|\n______________UUGUUUACGC\n3'-UUU...UACUA__________GCAGAAAG-5'\n_____________\|__________\|\n_____________19_________8\n	199 -- 205	9 -- 15	-13.3675 kcal/mol	1.73119 kcal/mol	1.20319 kcal/mol	195 206@LB@ \| \|@LB@5'-UAA...GAGGG AUAUC...UGC-3'@LB@ AACAGAUGCG@LB@ \|\|\|\|:\|\|\|\|\|@LB@ UUGUUUACGC@LB@3'-UUU...UACUA GCAGAAAG-5'@LB@ \| \|@LB@ 19 8@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -13.3675 kcal/mol@LB@Unfolding Energy - mRNA 1.73119 kcal/mol@LB@Unfolding Energy - sRNA 1.20319 kcal/mol@LB@@LB@Position - mRNA 196 -- 205@LB@Position - sRNA 9 -- 18@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 9 -- 15@LB@
196	0.01921	0.3104	b2167	fruA	-9.92	0.125082	150 -- 163	5 -- 22	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________149________________164\n_____________\|__________________\|\n5'-CGC...CGCAA__________________GACUU...AAA-3'\n______________UGAUGGC____GCGCGUC\n______________\|\|\|\|::\|____\|\|\|\|\|\|\|\n______________ACUAUUG____CGCGCAG\n3'-UUU...CUACU_______UUUA_______AAAG-5'\n_____________\|__________________\|\n_____________23_________________4\n	157 -- 163	5 -- 11	-18.2874 kcal/mol	7.11819 kcal/mol	1.25155 kcal/mol	149 164@LB@ \| \|@LB@5'-CGC...CGCAA GACUU...AAA-3'@LB@ UGAUGGC GCGCGUC@LB@ \|\|\|\|::\| \|\|\|\|\|\|\|@LB@ ACUAUUG CGCGCAG@LB@3'-UUU...CUACU UUUA AAAG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -18.2874 kcal/mol@LB@Unfolding Energy - mRNA 7.11819 kcal/mol@LB@Unfolding Energy - sRNA 1.25155 kcal/mol@LB@@LB@Position - mRNA 150 -- 163@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 5 -- 11@LB@
197	0.01929	0.3104	b2185	rplY	-8.58	0.206984	8 -- 20	7 -- 19	50S ribosomal subunit protein L25	_____________7_____________21\n_____________\|_____________\|\n____5'-CCAGUAC_____________AAAAA...GCA-3'\n______________UGGCAGGUGCGUG\n______________\|::\|\|::\|\|\|\|:\|\n______________AUUGUUUACGCGC\n3'-UUU...CUACU_____________AGAAAG-5'\n_____________\|_____________\|\n_____________20____________6\n	14 -- 20	7 -- 13	-17.3397 kcal/mol	7.54262 kcal/mol	1.21943 kcal/mol	7 21@LB@ \| \|@LB@ 5'-CCAGUAC AAAAA...GCA-3'@LB@ UGGCAGGUGCGUG@LB@ \|::\|\|::\|\|\|\|:\|@LB@ AUUGUUUACGCGC@LB@3'-UUU...CUACU AGAAAG-5'@LB@ \| \|@LB@ 20 6@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -17.3397 kcal/mol@LB@Unfolding Energy - mRNA 7.54262 kcal/mol@LB@Unfolding Energy - sRNA 1.21943 kcal/mol@LB@@LB@Position - mRNA 8 -- 20@LB@Position - sRNA 7 -- 19@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 7 -- 13@LB@
198	0.0193	0.3104	b2961	mutY	-10.33	0.106403	22 -- 38	1 -- 15	adenine DNA glycosylase	_____________21________________39\n_____________\|_________________\|\n5'-CGU...CGGUG_____A__U________AUAAA...UAU-3'\n______________AAAUG_CG_CGUUUUUC\n______________\|\|\|\|\|_\|\|_\|\|\|:\|\|\|\|\n______________UUUAC_GC_GCAGAAAG\n3'-UUU...UAUUG_________________-5'\n_____________\|________________\|\n_____________16_______________1\n	32 -- 38	1 -- 7	-14.8981 kcal/mol	3.3462 kcal/mol	1.21803 kcal/mol	21 39@LB@ \| \|@LB@5'-CGU...CGGUG A U AUAAA...UAU-3'@LB@ AAAUG CG CGUUUUUC@LB@ \|\|\|\|\| \|\| \|\|\|:\|\|\|\|@LB@ UUUAC GC GCAGAAAG@LB@3'-UUU...UAUUG -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -14.8981 kcal/mol@LB@Unfolding Energy - mRNA 3.3462 kcal/mol@LB@Unfolding Energy - sRNA 1.21803 kcal/mol@LB@@LB@Position - mRNA 22 -- 38@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 1 -- 7@LB@
199	0.01944	0.3104	b3657	yicJ	-13.22	0.033173	129 -- 161	8 -- 45	putative transporter	_____________128_____________________________________162\n_____________\|_______________________________________\|\n5'-CAG...GAAUA_________CA_____________UU____A________UAUCG...UGU-3'\n______________UUCG_CUCU_____CAGGGAUGGU____AC_AAAUGCGU\n______________\|\|\|:_\|\|\|\|_____\|\|\|\|\|\|\|\|:\|____\|\|_\|\|\|\|\|\|\|:\n______________AAGU_GAGA_____GUCCCUACUA____UG_UUUACGCG\n3'-UUU...UUUUA____A____CUUAA__________CUAU___________CAGAAAG-5'\n_____________\|_______________________________________\|\n_____________46______________________________________7\n	155 -- 161	8 -- 14	-30.3918 kcal/mol	7.7216 kcal/mol	9.45195 kcal/mol	128 162@LB@ \| \|@LB@5'-CAG...GAAUA CA UU A UAUCG...UGU-3'@LB@ UUCG CUCU CAGGGAUGGU AC AAAUGCGU@LB@ \|\|\|: \|\|\|\| \|\|\|\|\|\|\|\|:\| \|\| \|\|\|\|\|\|\|:@LB@ AAGU GAGA GUCCCUACUA UG UUUACGCG@LB@3'-UUU...UUUUA A CUUAA CUAU CAGAAAG-5'@LB@ \| \|@LB@ 46 7@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -30.3918 kcal/mol@LB@Unfolding Energy - mRNA 7.7216 kcal/mol@LB@Unfolding Energy - sRNA 9.45195 kcal/mol@LB@@LB@Position - mRNA 129 -- 161@LB@Position - sRNA 8 -- 45@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 8 -- 14@LB@
200	0.0195	0.3104	b3183	obgE	-7.01	0.355777	76 -- 83	4 -- 11	GTPase involved in cell partioning and DNA repair	_____________75_______84\n_____________\|________\|\n5'-UUU...UCUCG________GUCGU...GCC-3'\n______________GUGCGUUU\n______________\|:\|\|\|\|:\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	77 -- 83	4 -- 10	-11.428 kcal/mol	3.26207 kcal/mol	1.15639 kcal/mol	75 84@LB@ \| \|@LB@5'-UUU...UCUCG GUCGU...GCC-3'@LB@ GUGCGUUU@LB@ \|:\|\|\|\|:\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.01 kcal/mol@LB@Hybridization Energy -11.428 kcal/mol@LB@Unfolding Energy - mRNA 3.26207 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 4 -- 10@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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