Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
168	0.01219	0.2504	b1830	prc	-10.01	0.273454	1 -- 12	6 -- 17	carboxy-terminal protease for penicillin-binding protein 3	______________1___________13\n______________\|___________\|\n___________5'-_______C____CACCC...CGG-3'\n______________CGAAGAA_AGCA\n______________\|:\|\|\|\|\|_\|\|\|\|\n______________GUUUCUU_UCGU\n3'-UUU...CUGUA_______U____CACCG-5'\n_____________\|____________\|\n_____________18___________5\n	1 -- 7	11 -- 17	-11.3077 kcal/mol	0.751361 kcal/mol	0.542636 kcal/mol	1 13@LB@ \| \|@LB@ 5'- C CACCC...CGG-3'@LB@ CGAAGAA AGCA@LB@ \|:\|\|\|\|\| \|\|\|\|@LB@ GUUUCUU UCGU@LB@3'-UUU...CUGUA U CACCG-5'@LB@ \| \|@LB@ 18 5@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -11.3077 kcal/mol@LB@Unfolding Energy - mRNA 0.751361 kcal/mol@LB@Unfolding Energy - sRNA 0.542636 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 6 -- 17@LB@Position Seed - mRNA 1 -- 7@LB@Position Seed - sRNA 11 -- 17@LB@
11	0.0003708	0.1087	b4201	priB	-14.90	0.029310	176 -- 193	6 -- 26	primosomal protein N	_____________175___________________194\n_____________\|_____________________\|\n5'-AGG...GAAGC__________U__________AUUUC...AUC-3'\n______________UGGGGAU_UC___GAAGAGUA\n______________\|\|\|\|\|\|:_\|\|___\|\|\|:\|\|:\|\n______________ACCCCUG_AG___CUUUUCGU\n3'-UUU...GUUUU_______U__UUU________CACCG-5'\n_____________\|_____________________\|\n_____________27____________________5\n	187 -- 193	6 -- 12	-19.0189 kcal/mol	3.41067 kcal/mol	0.706421 kcal/mol	175 194@LB@ \| \|@LB@5'-AGG...GAAGC U AUUUC...AUC-3'@LB@ UGGGGAU UC GAAGAGUA@LB@ \|\|\|\|\|\|: \|\| \|\|\|:\|\|:\|@LB@ ACCCCUG AG CUUUUCGU@LB@3'-UUU...GUUUU U UUU CACCG-5'@LB@ \| \|@LB@ 27 5@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -19.0189 kcal/mol@LB@Unfolding Energy - mRNA 3.41067 kcal/mol@LB@Unfolding Energy - sRNA 0.706421 kcal/mol@LB@@LB@Position - mRNA 176 -- 193@LB@Position - sRNA 6 -- 26@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 6 -- 12@LB@
29	0.00125	0.1512	b2499	purM	-15.92	0.016248	173 -- 203	3 -- 34	phosphoribosylaminoimidazole synthetase	_____________172____________________________________204\n_____________\|______________________________________\|\n5'-UAU...UUCUA_______UAACGC________CC_______________ACCGA...CGC-3'\n______________CCGCAAG______GUGGGGAC_________AAGCAGUG\n______________\|\|:\|\|\|:______:\|\|\|\|\|\|\|_________\|\|\|\|\|\|\|\|\n______________GGUGUUU______UACCCCUG_________UUCGUCAC\n3'-UUU...CCCGA_____________________UAGUUUCUU________CG-5'\n_____________\|______________________________________\|\n_____________35_____________________________________2\n	197 -- 203	3 -- 9	-29.7141 kcal/mol	9.52212 kcal/mol	4.26884 kcal/mol	172 204@LB@ \| \|@LB@5'-UAU...UUCUA UAACGC CC ACCGA...CGC-3'@LB@ CCGCAAG GUGGGGAC AAGCAGUG@LB@ \|\|:\|\|\|: :\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GGUGUUU UACCCCUG UUCGUCAC@LB@3'-UUU...CCCGA UAGUUUCUU CG-5'@LB@ \| \|@LB@ 35 2@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -29.7141 kcal/mol@LB@Unfolding Energy - mRNA 9.52212 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 173 -- 203@LB@Position - sRNA 3 -- 34@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
60	0.003101	0.1789	b1849	purT	-10.92	0.194410	188 -- 196	17 -- 25	phosphoribosylglycinamide formyltransferase 2	_____________187_______197\n_____________\|_________\|\n5'-UUU...AAUCA_________CGUUA...GUC-3'\n______________GGGGAUAUU\n______________\|\|\|\|\|:\|\|:\n______________CCCCUGUAG\n3'-UUU...UUUUA_________UUUCU...CCG-5'\n_____________\|_________\|\n_____________26________16\n	190 -- 196	17 -- 23	-14.1846 kcal/mol	2.60139 kcal/mol	0.664736 kcal/mol	187 197@LB@ \| \|@LB@5'-UUU...AAUCA CGUUA...GUC-3'@LB@ GGGGAUAUU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCUGUAG@LB@3'-UUU...UUUUA UUUCU...CCG-5'@LB@ \| \|@LB@ 26 16@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -14.1846 kcal/mol@LB@Unfolding Energy - mRNA 2.60139 kcal/mol@LB@Unfolding Energy - sRNA 0.664736 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 17 -- 25@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 17 -- 23@LB@
165	0.01211	0.2504	b3642	pyrE	-11.74	0.138291	22 -- 41	7 -- 25	orotate phosphoribosyltransferase	_____________21___________________42\n_____________\|____________________\|\n5'-CGG...GUGCA_______GCA_____C____CGUUC...AUU-3'\n______________GGGGACG___GAAGG_GAGC\n______________\|\|\|\|\|\|:___:\|\|\|:_:\|\|\|\n______________CCCCUGU___UUUCU_UUCG\n3'-UUU...UUUUA_______AG______U____UCACCG-5'\n_____________\|____________________\|\n_____________26___________________6\n	22 -- 28	19 -- 25	-22.5653 kcal/mol	10.1153 kcal/mol	0.70626 kcal/mol	21 42@LB@ \| \|@LB@5'-CGG...GUGCA GCA C CGUUC...AUU-3'@LB@ GGGGACG GAAGG GAGC@LB@ \|\|\|\|\|\|: :\|\|\|: :\|\|\|@LB@ CCCCUGU UUUCU UUCG@LB@3'-UUU...UUUUA AG U UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -22.5653 kcal/mol@LB@Unfolding Energy - mRNA 10.1153 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 22 -- 41@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 19 -- 25@LB@
1	0	0	b3752	rbsK	-20.54	0.000534	137 -- 155	1 -- 21	ribokinase	_____________136___________________156\n_____________\|_____________________\|\n5'-GCA...GUGUA_____________________ACGCG...GUA-3'\n______________AUA_UAAAGAAAAGCAG_GGC\n______________\|:\|_:\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\n______________UGU_GUUUCUUUUCGUC_CCG\n3'-UUU...ACCCC___A_____________A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	146 -- 152	5 -- 11	-23.5677 kcal/mol	1.51892 kcal/mol	1.51103 kcal/mol	136 156@LB@ \| \|@LB@5'-GCA...GUGUA ACGCG...GUA-3'@LB@ AUA UAAAGAAAAGCAG GGC@LB@ \|:\| :\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|@LB@ UGU GUUUCUUUUCGUC CCG@LB@3'-UUU...ACCCC A A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -20.54 kcal/mol@LB@Hybridization Energy -23.5677 kcal/mol@LB@Unfolding Energy - mRNA 1.51892 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 137 -- 155@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 5 -- 11@LB@
98	0.006107	0.2179	b3822	recQ	-9.35	0.343777	185 -- 205	1 -- 22	ATP-dependent DNA helicase	_____________184_____________________206\n_____________\|_______________________\|\n5'-CGC...UUUCA___A_______U___U_______GCAGG...UUA-3'\n______________GGC_AUCGGGG_GAA___GUGGC\n______________\|:\|_\|\|\|:::\|_:\|\|___\|\|\|\|\|\n______________CUG_UAGUUUC_UUU___CACCG\n3'-UUU...UACCC___________U___CGU_____-5'\n_____________\|______________________\|\n_____________23_____________________1\n	189 -- 195	13 -- 19	-17.8698 kcal/mol	6.98341 kcal/mol	1.54023 kcal/mol	184 206@LB@ \| \|@LB@5'-CGC...UUUCA A U U GCAGG...UUA-3'@LB@ GGC AUCGGGG GAA GUGGC@LB@ \|:\| \|\|\|:::\| :\|\| \|\|\|\|\|@LB@ CUG UAGUUUC UUU CACCG@LB@3'-UUU...UACCC U CGU -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -9.35 kcal/mol@LB@Hybridization Energy -17.8698 kcal/mol@LB@Unfolding Energy - mRNA 6.98341 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 185 -- 205@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 13 -- 19@LB@
50	0.002349	0.1648	b2040	rfbD	-20.63	0.000491	127 -- 157	3 -- 32	dTDP-L-rhamnose synthase NAD(P)-dependent dTDP-4-dehydrorhamnose reductase subunit	_____________126______________________________158\n_____________\|________________________________\|\n5'-GAU...CCAAU__________UU____AUGU____________CCUAU...CUA-3'\n______________ACAAAAUGGG__GAUA_____GAAAAGUGGUG\n______________\|\|\|\|\|\|\|\|\|\|__\|\|:\|_____\|\|\|\|\|\|::\|\|\|\n______________UGUUUUACCC__CUGU_____CUUUUCGUCAC\n3'-UUU...CGAGG________________AGUUU___________CG-5'\n_____________\|________________________________\|\n_____________33_______________________________2\n	151 -- 157	3 -- 9	-27.2371 kcal/mol	4.0691 kcal/mol	2.53925 kcal/mol	126 158@LB@ \| \|@LB@5'-GAU...CCAAU UU AUGU CCUAU...CUA-3'@LB@ ACAAAAUGGG GAUA GAAAAGUGGUG@LB@ \|\|\|\|\|\|\|\|\|\| \|\|:\| \|\|\|\|\|\|::\|\|\|@LB@ UGUUUUACCC CUGU CUUUUCGUCAC@LB@3'-UUU...CGAGG AGUUU CG-5'@LB@ \| \|@LB@ 33 2@LB@@LB@@LB@Energy -20.63 kcal/mol@LB@Hybridization Energy -27.2371 kcal/mol@LB@Unfolding Energy - mRNA 4.0691 kcal/mol@LB@Unfolding Energy - sRNA 2.53925 kcal/mol@LB@@LB@Position - mRNA 127 -- 157@LB@Position - sRNA 3 -- 32@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 3 -- 9@LB@
158	0.01161	0.2504	b3907	rhaT	-15.90	0.016445	218 -- 234	1 -- 28	L-rhamnose:proton symporter	_____________217__________________________235\n_____________\|____________________________\|\n5'-AUG...AUUAC____________U_______________AUUUG...CAU-3'\n______________GAUGGGGAUAUU____________UGGC\n______________:\|\|\|\|\|\|\|:\|\|:____________\|\|\|\|\n______________UUACCCCUGUAG____________ACCG\n3'-UUU...GUGUU____________UUUCUUUUCGUC____-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	223 -- 229	17 -- 23	-20.3321 kcal/mol	1.91011 kcal/mol	2.519 kcal/mol	217 235@LB@ \| \|@LB@5'-AUG...AUUAC U AUUUG...CAU-3'@LB@ GAUGGGGAUAUU UGGC@LB@ :\|\|\|\|\|\|\|:\|\|: \|\|\|\|@LB@ UUACCCCUGUAG ACCG@LB@3'-UUU...GUGUU UUUCUUUUCGUC -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -20.3321 kcal/mol@LB@Unfolding Energy - mRNA 1.91011 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 218 -- 234@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 17 -- 23@LB@
46	0.002205	0.1648	b1662	ribC	-17.71	0.005126	34 -- 61	2 -- 29	riboflavin synthase alpha subunit	_____________33_____________________________62\n_____________\|______________________________\|\n5'-UUU...CGCCU_______CA___A_____A___________GAAAU...UGG-3'\n______________GAAUGGG__GCA__AAAG_AGAAGCAG_GG\n______________:\|\|\|\|\|\|__:\|\|__\|\|\|\|_\|:\|\|\|\|\|\|_\|\|\n______________UUUACCC__UGU__UUUC_UUUUCGUC_CC\n3'-UUU...GGUGU_______C____AG_____________A__G-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	53 -- 59	5 -- 11	-25.8778 kcal/mol	5.65259 kcal/mol	2.51906 kcal/mol	33 62@LB@ \| \|@LB@5'-UUU...CGCCU CA A A GAAAU...UGG-3'@LB@ GAAUGGG GCA AAAG AGAAGCAG GG@LB@ :\|\|\|\|\|\| :\|\| \|\|\|\| \|:\|\|\|\|\|\| \|\|@LB@ UUUACCC UGU UUUC UUUUCGUC CC@LB@3'-UUU...GGUGU C AG A G-5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -17.71 kcal/mol@LB@Hybridization Energy -25.8778 kcal/mol@LB@Unfolding Energy - mRNA 5.65259 kcal/mol@LB@Unfolding Energy - sRNA 2.51906 kcal/mol@LB@@LB@Position - mRNA 34 -- 61@LB@Position - sRNA 2 -- 29@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@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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