Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
170	0.01916	0.363	b1202	ycgV	-6.78	0.125661	82 -- 88	39 -- 45	putative adhesin	b2647	_____________81______89\n_____________\|_______\|\n5'-ACU...UCUCU_______UCAUC...UUG-3'\n______________GAGAAGC\n______________:\|\|\|\|\|\|\n______________UUCUUCG\n3'-UUU...AUUCG_______UGAAU...CAA-5'\n_____________\|_______\|\n_____________46______38\n	82 -- 88	39 -- 45	-7.60605 kcal/mol	0.31609 kcal/mol	0.514773 kcal/mol	81 89@LB@ \| \|@LB@5'-ACU...UCUCU UCAUC...UUG-3'@LB@ GAGAAGC@LB@ :\|\|\|\|\|\|@LB@ UUCUUCG@LB@3'-UUU...AUUCG UGAAU...CAA-5'@LB@ \| \|@LB@ 46 38@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -7.60605 kcal/mol@LB@Unfolding Energy - mRNA 0.31609 kcal/mol@LB@Unfolding Energy - sRNA 0.514773 kcal/mol@LB@@LB@Position - mRNA 82 -- 88@LB@Position - sRNA 39 -- 45@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 39 -- 45@LB@
200	0.02417	0.3893	b1747	astA	-6.36	0.159223	49 -- 56	39 -- 46	arginine succinyltransferase		_____________48_______57\n_____________\|________\|\n5'-GGC...UCUCU________GGCGA...AAG-3'\n______________CAGGAAGC\n______________\|\|:\|\|\|\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	50 -- 56	39 -- 45	-10.5455 kcal/mol	1.56403 kcal/mol	2.62555 kcal/mol	48 57@LB@ \| \|@LB@5'-GGC...UCUCU GGCGA...AAG-3'@LB@ CAGGAAGC@LB@ \|\|:\|\|\|\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -6.36 kcal/mol@LB@Hybridization Energy -10.5455 kcal/mol@LB@Unfolding Energy - mRNA 1.56403 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 49 -- 56@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 39 -- 45@LB@
107	0.009263	0.2693	b3034	nudF	-7.86	0.065629	202 -- 214	42 -- 54	ADP-ribose pyrophosphatase		_____________201___________215\n_____________\|_____________\|\n5'-AUU...AACAA_________C___CAACC...UUU-3'\n______________UGCUUAAGC_AGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\n______________ACGAAUUCG_UCU\n3'-UUU...UUUGA_________U___UCGUG...CAA-5'\n_____________\|_____________\|\n_____________55____________41\n	204 -- 210	46 -- 52	-15.7149 kcal/mol	1.83586 kcal/mol	6.01534 kcal/mol	201 215@LB@ \| \|@LB@5'-AUU...AACAA C CAACC...UUU-3'@LB@ UGCUUAAGC AGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|@LB@ ACGAAUUCG UCU@LB@3'-UUU...UUUGA U UCGUG...CAA-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -15.7149 kcal/mol@LB@Unfolding Energy - mRNA 1.83586 kcal/mol@LB@Unfolding Energy - sRNA 6.01534 kcal/mol@LB@@LB@Position - mRNA 202 -- 214@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 46 -- 52@LB@
171	0.01957	0.3668	b2498	upp	-5.84	0.210430	244 -- 265	42 -- 61	uracil phosphoribosyltransferase		_____________243____________________266\n_____________\|______________________\|\n5'-GGC...CAAGC_______GA___G_________UAUCA...CCG-3'\n______________UGGGACU__UGC_UGAGCAAGA\n______________\|\|::\|\|\|__\|\|\|_\|:\|\|\|\|\|\|\|\n______________ACUUUGA__ACG_AUUCGUUCU\n3'-UUU...GCCCU____________A_________UCGUG...CAA-5'\n_____________\|______________________\|\n_____________62_____________________41\n	259 -- 265	42 -- 48	-21.1169 kcal/mol	8.03919 kcal/mol	7.23689 kcal/mol	243 266@LB@ \| \|@LB@5'-GGC...CAAGC GA G UAUCA...CCG-3'@LB@ UGGGACU UGC UGAGCAAGA@LB@ \|\|::\|\|\| \|\|\| \|:\|\|\|\|\|\|\|@LB@ ACUUUGA ACG AUUCGUUCU@LB@3'-UUU...GCCCU A UCGUG...CAA-5'@LB@ \| \|@LB@ 62 41@LB@@LB@@LB@Energy -5.84 kcal/mol@LB@Hybridization Energy -21.1169 kcal/mol@LB@Unfolding Energy - mRNA 8.03919 kcal/mol@LB@Unfolding Energy - sRNA 7.23689 kcal/mol@LB@@LB@Position - mRNA 244 -- 265@LB@Position - sRNA 42 -- 61@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 42 -- 48@LB@
120	0.01039	0.2788	b2314	dedD	-6.27	0.167184	42 -- 54	45 -- 58	membrane-anchored periplasmic protein involved in septation		_____________41_____________55\n_____________\|______________\|\n5'-UUG...AGAAC______________UUUGG...AUU-3'\n______________AAC_UGCUUGAGCA\n______________\|\|\|_\|\|\|\|\|:\|\|\|\|\n______________UUG_ACGAAUUCGU\n3'-UUU...CUACU___A__________UCUUC...CAA-5'\n_____________\|______________\|\n_____________59_____________44\n	47 -- 53	46 -- 52	-15.7533 kcal/mol	3.46622 kcal/mol	6.01947 kcal/mol	41 55@LB@ \| \|@LB@5'-UUG...AGAAC UUUGG...AUU-3'@LB@ AAC UGCUUGAGCA@LB@ \|\|\| \|\|\|\|\|:\|\|\|\|@LB@ UUG ACGAAUUCGU@LB@3'-UUU...CUACU A UCUUC...CAA-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -15.7533 kcal/mol@LB@Unfolding Energy - mRNA 3.46622 kcal/mol@LB@Unfolding Energy - sRNA 6.01947 kcal/mol@LB@@LB@Position - mRNA 42 -- 54@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 46 -- 52@LB@
183	0.02165	0.3768	b4201	priB	-4.41	0.419305	289 -- 298	45 -- 54	primosomal protein N		_____________288________299\n_____________\|__________\|\n5'-AGG...GUUCG__________UC-3'\n______________UGCUUGAGCA\n______________\|\|\|\|\|:\|\|\|\|\n______________ACGAAUUCGU\n3'-UUU...UUUGA__________UCUUC...CAA-5'\n_____________\|__________\|\n_____________55_________44\n	290 -- 296	47 -- 53	-14.7774 kcal/mol	4.46723 kcal/mol	5.90361 kcal/mol	288 299@LB@ \| \|@LB@5'-AGG...GUUCG UC-3'@LB@ UGCUUGAGCA@LB@ \|\|\|\|\|:\|\|\|\|@LB@ ACGAAUUCGU@LB@3'-UUU...UUUGA UCUUC...CAA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -4.41 kcal/mol@LB@Hybridization Energy -14.7774 kcal/mol@LB@Unfolding Energy - mRNA 4.46723 kcal/mol@LB@Unfolding Energy - sRNA 5.90361 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 47 -- 53@LB@
196	0.02353	0.3864	b1948	fliP	-9.61	0.021211	171 -- 185	45 -- 59	flagellar biosynthesis protein		_____________170_____________186\n_____________\|_______________\|\n5'-AUU...AUGAA_______________UAGCG...GCG-3'\n______________AAAUUUGCUUAAGCG\n______________\|\|\|:\|\|\|\|\|\|\|\|\|\|:\n______________UUUGAACGAAUUCGU\n3'-UUU...CCUAC_______________UCUUC...CAA-5'\n_____________\|_______________\|\n_____________60______________44\n	178 -- 184	46 -- 52	-18.3894 kcal/mol	2.75936 kcal/mol	6.02152 kcal/mol	170 186@LB@ \| \|@LB@5'-AUU...AUGAA UAGCG...GCG-3'@LB@ AAAUUUGCUUAAGCG@LB@ \|\|\|:\|\|\|\|\|\|\|\|\|\|:@LB@ UUUGAACGAAUUCGU@LB@3'-UUU...CCUAC UCUUC...CAA-5'@LB@ \| \|@LB@ 60 44@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -18.3894 kcal/mol@LB@Unfolding Energy - mRNA 2.75936 kcal/mol@LB@Unfolding Energy - sRNA 6.02152 kcal/mol@LB@@LB@Position - mRNA 171 -- 185@LB@Position - sRNA 45 -- 59@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 46 -- 52@LB@
154	0.01606	0.3359	b2587	kgtP	-4.55	0.394910	6 -- 12	52 -- 58	alpha-ketoglutarate transporter		_____________5_______13\n_____________\|_______\|\n______5'-UCCCC_______CCACU...UCG-3'\n______________AACUUGC\n______________\|\|\|\|\|\|\|\n______________UUGAACG\n3'-UUU...CUACU_______AAUUC...CAA-5'\n_____________\|_______\|\n_____________59______51\n	6 -- 12	52 -- 58	-7.82918 kcal/mol	0.15004 kcal/mol	3.13411 kcal/mol	5 13@LB@ \| \|@LB@ 5'-UCCCC CCACU...UCG-3'@LB@ AACUUGC@LB@ \|\|\|\|\|\|\|@LB@ UUGAACG@LB@3'-UUU...CUACU AAUUC...CAA-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -4.55 kcal/mol@LB@Hybridization Energy -7.82918 kcal/mol@LB@Unfolding Energy - mRNA 0.15004 kcal/mol@LB@Unfolding Energy - sRNA 3.13411 kcal/mol@LB@@LB@Position - mRNA 6 -- 12@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 52 -- 58@LB@
157	0.01701	0.3489	b3856	mobB	-4.94	0.329991	189 -- 197	52 -- 60	molybdopterin-guanine dinucleotide biosynthesis protein B		_____________188_______198\n_____________\|_________\|\n5'-GUG...CCAGA_________CCGAU...CCA-3'\n______________GGAGCUUGC\n______________\|:\|:\|\|\|\|\|\n______________CUUUGAACG\n3'-UUU...CCCUA_________AAUUC...CAA-5'\n_____________\|_________\|\n_____________61________51\n	191 -- 197	52 -- 58	-10.6989 kcal/mol	2.59286 kcal/mol	3.16562 kcal/mol	188 198@LB@ \| \|@LB@5'-GUG...CCAGA CCGAU...CCA-3'@LB@ GGAGCUUGC@LB@ \|:\|:\|\|\|\|\|@LB@ CUUUGAACG@LB@3'-UUU...CCCUA AAUUC...CAA-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -4.94 kcal/mol@LB@Hybridization Energy -10.6989 kcal/mol@LB@Unfolding Energy - mRNA 2.59286 kcal/mol@LB@Unfolding Energy - sRNA 3.16562 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 52 -- 58@LB@
99	0.007347	0.239	b4348	hsdS	-4.18	0.460078	133 -- 139	70 -- 76	specificity determinant for hsdM and hsdR		_____________132_____140\n_____________\|_______\|\n5'-CUG...GUGAA_______CGAGC...UAA-3'\n______________CUGGGGG\n______________\|\|\|:\|\|\|\n______________GACUCCC\n3'-UUU...GCUGG_______CCAGC...CAA-5'\n_____________\|_______\|\n_____________77______69\n	133 -- 139	70 -- 76	-10.3039 kcal/mol	2.51492 kcal/mol	3.60488 kcal/mol	132 140@LB@ \| \|@LB@5'-CUG...GUGAA CGAGC...UAA-3'@LB@ CUGGGGG@LB@ \|\|\|:\|\|\|@LB@ GACUCCC@LB@3'-UUU...GCUGG CCAGC...CAA-5'@LB@ \| \|@LB@ 77 69@LB@@LB@@LB@Energy -4.18 kcal/mol@LB@Hybridization Energy -10.3039 kcal/mol@LB@Unfolding Energy - mRNA 2.51492 kcal/mol@LB@Unfolding Energy - sRNA 3.60488 kcal/mol@LB@@LB@Position - mRNA 133 -- 139@LB@Position - sRNA 70 -- 76@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 70 -- 76@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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