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	Additional homologs
128	0.00928	0.2491	b0491	fetB	-12.70	0.090276	178 -- 195	1 -- 17	iron export ABC transporter permease; peroxide resistance protein		_____________177________________196\n_____________\|__________________\|\n5'-GCC...CAUGC________U____GAA__ACGCU...AGA-3'\n______________CGGAGAAA_GCAG___GC\n______________\|::\|\|\|\|\|_\|\|\|\|___\|\|\n______________GUUUCUUU_CGUC___CG\n3'-UUU...CUGUA________U____AC___-5'\n_____________\|_________________\|\n_____________18________________1\n	179 -- 185	10 -- 16	-17.1669 kcal/mol	3.03232 kcal/mol	1.43853 kcal/mol	177 196@LB@ \| \|@LB@5'-GCC...CAUGC U GAA ACGCU...AGA-3'@LB@ CGGAGAAA GCAG GC@LB@ \|::\|\|\|\|\| \|\|\|\| \|\|@LB@ GUUUCUUU CGUC CG@LB@3'-UUU...CUGUA U AC -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -17.1669 kcal/mol@LB@Unfolding Energy - mRNA 3.03232 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 10 -- 16@LB@
129	0.009293	0.2491	b0428	cyoE	-12.51	0.098557	18 -- 26	1 -- 9	protoheme IX farnesyltransferase		_____________17________27\n_____________\|_________\|\n5'-GGA...GCAAU_________ACAGG...GCA-3'\n______________GGCAGUGGU\n______________:\|\|\|\|\|\|\|:\n______________UCGUCACCG\n3'-UUU...UCUUU_________-5'\n_____________\|________\|\n_____________10_______1\n	20 -- 26	1 -- 7	-15.8954 kcal/mol	2.13019 kcal/mol	1.2588 kcal/mol	17 27@LB@ \| \|@LB@5'-GGA...GCAAU ACAGG...GCA-3'@LB@ GGCAGUGGU@LB@ :\|\|\|\|\|\|\|:@LB@ UCGUCACCG@LB@3'-UUU...UCUUU -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -12.51 kcal/mol@LB@Hybridization Energy -15.8954 kcal/mol@LB@Unfolding Energy - mRNA 2.13019 kcal/mol@LB@Unfolding Energy - sRNA 1.2588 kcal/mol@LB@@LB@Position - mRNA 18 -- 26@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 1 -- 7@LB@
131	0.009354	0.2491	b4478	dgoD	-14.24	0.041949	180 -- 199	1 -- 22	D-galactonate dehydratase		_____________179____________________200\n_____________\|______________________\|\n5'-AAA...GUUAA_____AUC______________AAUGA...UGA-3'\n______________GGCGU____GAGAGGCAGUG_C\n______________\|:\|:\|____\|\|:\|:\|\|\|\|\|\|_\|\n______________CUGUA____CUUUUCGUCAC_G\n3'-UUU...UACCC_____GUUU___________C_-5'\n_____________\|_____________________\|\n_____________23____________________1\n	192 -- 198	3 -- 9	-21.1696 kcal/mol	5.38995 kcal/mol	1.54023 kcal/mol	179 200@LB@ \| \|@LB@5'-AAA...GUUAA AUC AAUGA...UGA-3'@LB@ GGCGU GAGAGGCAGUG C@LB@ \|:\|:\| \|\|:\|:\|\|\|\|\|\| \|@LB@ CUGUA CUUUUCGUCAC G@LB@3'-UUU...UACCC GUUU C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -21.1696 kcal/mol@LB@Unfolding Energy - mRNA 5.38995 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 180 -- 199@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 3 -- 9@LB@
136	0.00981	0.2504	b4063	soxR	-14.24	0.041834	39 -- 60	1 -- 21	redox-sensitive transcriptional activator of soxS; autorepressor		_____________38_____________________61\n_____________\|______________________\|\n5'-GCA...CGACU_______U_UU______C____CAAUA...GUA-3'\n______________ACAUCAA_G__AAGCGG_UGGU\n______________\|\|\|\|\|\|\|_\|__\|\|\|\|:\|_\|\|\|:\n______________UGUAGUU_C__UUCGUC_ACCG\n3'-UUU...ACCCC_______U_UU___________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	39 -- 45	15 -- 21	-21.0533 kcal/mol	5.29766 kcal/mol	1.51103 kcal/mol	38 61@LB@ \| \|@LB@5'-GCA...CGACU U UU C CAAUA...GUA-3'@LB@ ACAUCAA G AAGCGG UGGU@LB@ \|\|\|\|\|\|\| \| \|\|\|\|:\| \|\|\|:@LB@ UGUAGUU C UUCGUC ACCG@LB@3'-UUU...ACCCC U UU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -21.0533 kcal/mol@LB@Unfolding Energy - mRNA 5.29766 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 39 -- 60@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 15 -- 21@LB@
137	0.0102	0.2504	b0957	ompA	-10.25	0.250752	198 -- 232	1 -- 30	outer membrane protein A (3a;II*;G;d)		_____________197_________________________________233\n_____________\|___________________________________\|\n5'-CUU...CGCAA______AAAAA____GCUAUCGC__UU________ACUGG...AAC-3'\n______________AAAAUG_____GACA________GA__GCAGUGGC\n______________\|\|\|\|\|\|_____\|\|\|\|________:\|__\|\|\|\|\|\|\|\|\n______________UUUUAC_____CUGU________UU__CGUCACCG\n3'-UUU...AGGUG______CC_______AGUUUC____UU________-5'\n_____________\|__________________________________\|\n_____________31_________________________________1\n	226 -- 232	1 -- 7	-21.624 kcal/mol	8.85247 kcal/mol	2.51911 kcal/mol	197 233@LB@ \| \|@LB@5'-CUU...CGCAA AAAAA GCUAUCGC UU ACUGG...AAC-3'@LB@ AAAAUG GACA GA GCAGUGGC@LB@ \|\|\|\|\|\| \|\|\|\| :\| \|\|\|\|\|\|\|\|@LB@ UUUUAC CUGU UU CGUCACCG@LB@3'-UUU...AGGUG CC AGUUUC UU -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -21.624 kcal/mol@LB@Unfolding Energy - mRNA 8.85247 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 198 -- 232@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 1 -- 7@LB@
138	0.0102	0.2504	b0830	gsiB	-12.88	0.082739	282 -- 298	1 -- 16	glutathione ABC transporter periplasmic binding protein		_____________281_______________299\n_____________\|_________________\|\n5'-GGC...CUGCC_____UGU_________GG-3'\n______________AAAGA___GGUGGUGGC\n______________\|\|\|\|\|___:\|::\|\|\|\|\|\n______________UUUCU___UCGUCACCG\n3'-UUU...UGUAG_____UU__________-5'\n_____________\|________________\|\n_____________17_______________1\n	292 -- 298	1 -- 7	-17.0557 kcal/mol	2.82856 kcal/mol	1.34555 kcal/mol	281 299@LB@ \| \|@LB@5'-GGC...CUGCC UGU GG-3'@LB@ AAAGA GGUGGUGGC@LB@ \|\|\|\|\| :\|::\|\|\|\|\|@LB@ UUUCU UCGUCACCG@LB@3'-UUU...UGUAG UU -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -17.0557 kcal/mol@LB@Unfolding Energy - mRNA 2.82856 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
140	0.01029	0.2504	b3247	rng	-10.20	0.255190	49 -- 63	1 -- 14	ribonuclease G		_____________48______________64\n_____________\|_______________\|\n5'-GUU...CCGUU___U_______GU__AUACG...CGC-3'\n______________AGA_AAAGCAG__GC\n______________\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________UCU_UUUCGUC__CG\n3'-UUU...UAGUU___________AC__-5'\n_____________\|______________\|\n_____________15_____________1\n	53 -- 59	5 -- 11	-13.7724 kcal/mol	2.22711 kcal/mol	1.34059 kcal/mol	48 64@LB@ \| \|@LB@5'-GUU...CCGUU U GU AUACG...CGC-3'@LB@ AGA AAAGCAG GC@LB@ \|\|\| \|\|\|\|\|\|\| \|\|@LB@ UCU UUUCGUC CG@LB@3'-UUU...UAGUU AC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -13.7724 kcal/mol@LB@Unfolding Energy - mRNA 2.22711 kcal/mol@LB@Unfolding Energy - sRNA 1.34059 kcal/mol@LB@@LB@Position - mRNA 49 -- 63@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
141	0.01037	0.2504	b2161	nupX	-15.31	0.023296	54 -- 80	1 -- 26	nucleoside permease	b2164	_____________53____________________________81\n_____________\|_____________________________\|\n5'-UUG...GGUUC_______UA_________U_______C__GGCUA...GCG-3'\n______________UGGGGAU__GUCGAAGAG__GC_GUG_GC\n______________\|\|\|\|\|\|:__:\|\|:\|\|\|\|:__\|\|_\|\|\|_\|\|\n______________ACCCCUG__UAGUUUCUU__CG_CAC_CG\n3'-UUU...GUUUU__________________UU__U______-5'\n_____________\|____________________________\|\n_____________27___________________________1\n	65 -- 71	11 -- 17	-27.7009 kcal/mol	9.87339 kcal/mol	2.51842 kcal/mol	53 81@LB@ \| \|@LB@5'-UUG...GGUUC UA U C GGCUA...GCG-3'@LB@ UGGGGAU GUCGAAGAG GC GUG GC@LB@ \|\|\|\|\|\|: :\|\|:\|\|\|\|: \|\| \|\|\| \|\|@LB@ ACCCCUG UAGUUUCUU CG CAC CG@LB@3'-UUU...GUUUU UU U -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -27.7009 kcal/mol@LB@Unfolding Energy - mRNA 9.87339 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 54 -- 80@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 11 -- 17@LB@
143	0.01049	0.2504	b1004	wrbA	-9.61	0.314473	272 -- 293	1 -- 25	NAD(P)H:quinone oxidoreductase		_____________271________________________294\n_____________\|__________________________\|\n5'-UUA...GCUGA___U_________C_______A____GCUGAAG-3'\n______________GGG_GCA____AG_AAAGUGG_UGGC\n______________\|\|\|_:\|\|____\|\|_\|\|\|\|::\|_\|\|\|\|\n______________CCC_UGU____UC_UUUCGUC_ACCG\n3'-UUU...UUUUA___C___AGUU__U____________-5'\n_____________\|_________________________\|\n_____________26________________________1\n	282 -- 288	5 -- 11	-20.1219 kcal/mol	7.99134 kcal/mol	2.51748 kcal/mol	271 294@LB@ \| \|@LB@5'-UUA...GCUGA U C A GCUGAAG-3'@LB@ GGG GCA AG AAAGUGG UGGC@LB@ \|\|\| :\|\| \|\| \|\|\|\|::\| \|\|\|\|@LB@ CCC UGU UC UUUCGUC ACCG@LB@3'-UUU...UUUUA C AGUU U -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -20.1219 kcal/mol@LB@Unfolding Energy - mRNA 7.99134 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 272 -- 293@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 5 -- 11@LB@
144	0.01052	0.2504	b1066	rimJ	-12.60	0.094480	174 -- 195	1 -- 22	ribosomal-protein-S5-alanine N-acetyltransferase		_____________173_____________________196\n_____________\|_______________________\|\n5'-AUU...UUAAA_______C___________A___AUAGA...AUU-3'\n______________GACGUUA_GGGAAGG_AGU_GGU\n______________\|\|\|:\|:\|_:\|:\|\|:\|_\|\|\|_\|\|:\n______________CUGUAGU_UCUUUUC_UCA_CCG\n3'-UUU...UACCC_______U_______G_______-5'\n_____________\|______________________\|\n_____________23_____________________1\n	182 -- 188	8 -- 14	-20.3318 kcal/mol	6.19349 kcal/mol	1.54023 kcal/mol	173 196@LB@ \| \|@LB@5'-AUU...UUAAA C A AUAGA...AUU-3'@LB@ GACGUUA GGGAAGG AGU GGU@LB@ \|\|\|:\|:\| :\|:\|\|:\| \|\|\| \|\|:@LB@ CUGUAGU UCUUUUC UCA CCG@LB@3'-UUU...UACCC U G -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -20.3318 kcal/mol@LB@Unfolding Energy - mRNA 6.19349 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 174 -- 195@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 8 -- 14@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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