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
101	0.01972	0.6177	b3636	rpmG	-7.41	0.136064	187 -- 193	44 -- 50	50S ribosomal subunit protein L33	_____________186_____194\n_____________\|_______\|\n5'-CAC...UACUU_______AUAAA...AAC-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	187 -- 193	44 -- 50	-8.97978 kcal/mol	0.747566 kcal/mol	0.825028 kcal/mol	186 194@LB@ \| \|@LB@5'-CAC...UACUU AUAAA...AAC-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -7.41 kcal/mol@LB@Hybridization Energy -8.97978 kcal/mol@LB@Unfolding Energy - mRNA 0.747566 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 187 -- 193@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 44 -- 50@LB@
128	0.02532	0.6177	b3642	pyrE	-8.06	0.101423	72 -- 92	43 -- 68	orotate phosphoribosyltransferase	_____________71_________________________93\n_____________\|__________________________\|\n5'-CGG...CUUGU_G___C____________________CGAAU...AUU-3'\n______________U_GCU__UGGCCCG____AGGGGAAU\n______________\|_\|\|\|__\|\|\|\|\|\|\|____\|\|:\|\|\|\|\|\n______________A_CGA__ACCGGGC____UCUCCUUA\n3'-UUU...GUUAU_G___UA_______AGUU________AAGUA...ACA-5'\n_____________\|__________________________\|\n_____________69_________________________42\n	86 -- 92	43 -- 49	-26.5136 kcal/mol	7.12642 kcal/mol	11.3306 kcal/mol	71 93@LB@ \| \|@LB@5'-CGG...CUUGU G C CGAAU...AUU-3'@LB@ U GCU UGGCCCG AGGGGAAU@LB@ \| \|\|\| \|\|\|\|\|\|\| \|\|:\|\|\|\|\|@LB@ A CGA ACCGGGC UCUCCUUA@LB@3'-UUU...GUUAU G UA AGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 69 42@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -26.5136 kcal/mol@LB@Unfolding Energy - mRNA 7.12642 kcal/mol@LB@Unfolding Energy - sRNA 11.3306 kcal/mol@LB@@LB@Position - mRNA 72 -- 92@LB@Position - sRNA 43 -- 68@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 43 -- 49@LB@
184	0.03803	0.6177	b3647	ligB	-3.67	0.590336	72 -- 111	39 -- 67	DNA ligase NAD(+)-dependent	_____________71________________________________________112\n_____________\|_________________________________________\|\n5'-GGC...GCUUC_______U________UUCACUGCAAUA____C__U_____GGAAG...AAA-3'\n______________CGC_AUU_GCCUGUCA____________AAGA_GA_UUUCA\n______________\|\|\|_\|\|\|_\|\|\|:\|\|\|\|____________\|\|\|\|_\|\|_\|\|\|\|\|\n______________GCG_UAA_CGGGCAGU____________UUCU_CU_AAAGU\n3'-UUU...UUAUA___A___C________________________C__U_____AAAAA...ACA-5'\n_____________\|_________________________________________\|\n_____________68________________________________________38\n	80 -- 86	52 -- 58	-24.1741 kcal/mol	6.974 kcal/mol	13.5271 kcal/mol	71 112@LB@ \| \|@LB@5'-GGC...GCUUC U UUCACUGCAAUA C U GGAAG...AAA-3'@LB@ CGC AUU GCCUGUCA AAGA GA UUUCA@LB@ \|\|\| \|\|\| \|\|\|:\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|@LB@ GCG UAA CGGGCAGU UUCU CU AAAGU@LB@3'-UUU...UUAUA A C C U AAAAA...ACA-5'@LB@ \| \|@LB@ 68 38@LB@@LB@@LB@Energy -3.67 kcal/mol@LB@Hybridization Energy -24.1741 kcal/mol@LB@Unfolding Energy - mRNA 6.974 kcal/mol@LB@Unfolding Energy - sRNA 13.5271 kcal/mol@LB@@LB@Position - mRNA 72 -- 111@LB@Position - sRNA 39 -- 67@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 52 -- 58@LB@
39	0.007917	0.6129	b3657	yicJ	-11.19	0.023423	220 -- 230	47 -- 57	putative transporter	_____________219_________231\n_____________\|___________\|\n5'-CAG...GUUGU___________AAAAU...UGU-3'\n______________CCGUUAAAGAG\n______________\|\|\|\|:\|\|\|\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	224 -- 230	47 -- 53	-15.9196 kcal/mol	1.98973 kcal/mol	2.73556 kcal/mol	219 231@LB@ \| \|@LB@5'-CAG...GUUGU AAAAU...UGU-3'@LB@ CCGUUAAAGAG@LB@ \|\|\|\|:\|\|\|\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -15.9196 kcal/mol@LB@Unfolding Energy - mRNA 1.98973 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 220 -- 230@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 47 -- 53@LB@
22	0.004195	0.5992	b3715	yieH	-7.44	0.134211	287 -- 299	41 -- 55	phosphoenolpyruvate and 6-phosphogluconate phosphatase	_____________286_____________300\n_____________\|_______________\|\n5'-CUG...ACGAU___UC__________G-3'\n______________GUU____AGGAAUUU\n______________\|\|:____\|\|\|\|\|\|\|\|\n______________CAG____UCCUUAAA\n3'-UUU...CCGGG___UUUC________GUAAA...ACA-5'\n_____________\|_______________\|\n_____________56______________40\n	293 -- 299	41 -- 47	-8.9861 kcal/mol	0.60049 kcal/mol	0.947844 kcal/mol	286 300@LB@ \| \|@LB@5'-CUG...ACGAU UC G-3'@LB@ GUU AGGAAUUU@LB@ \|\|: \|\|\|\|\|\|\|\|@LB@ CAG UCCUUAAA@LB@3'-UUU...CCGGG UUUC GUAAA...ACA-5'@LB@ \| \|@LB@ 56 40@LB@@LB@@LB@Energy -7.44 kcal/mol@LB@Hybridization Energy -8.9861 kcal/mol@LB@Unfolding Energy - mRNA 0.60049 kcal/mol@LB@Unfolding Energy - sRNA 0.947844 kcal/mol@LB@@LB@Position - mRNA 287 -- 299@LB@Position - sRNA 41 -- 55@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 41 -- 47@LB@
27	0.005027	0.5992	b3745	viaA	-10.46	0.033099	243 -- 253	42 -- 52	stimulator of RavA ATPase activity; von Willebrand factor domain protein	_____________242_________254\n_____________\|___________\|\n5'-ACG...UCAGC___________GAUCG...CGG-3'\n______________GAAGAGGGAUU\n______________:\|\|\|\|\|\|:\|\|\|\n______________UUUCUCCUUAA\n3'-UUU...GGCAG___________AGUAA...ACA-5'\n_____________\|___________\|\n_____________53__________41\n	247 -- 253	42 -- 48	-12.7293 kcal/mol	1.40033 kcal/mol	0.866923 kcal/mol	242 254@LB@ \| \|@LB@5'-ACG...UCAGC GAUCG...CGG-3'@LB@ GAAGAGGGAUU@LB@ :\|\|\|\|\|\|:\|\|\|@LB@ UUUCUCCUUAA@LB@3'-UUU...GGCAG AGUAA...ACA-5'@LB@ \| \|@LB@ 53 41@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -12.7293 kcal/mol@LB@Unfolding Energy - mRNA 1.40033 kcal/mol@LB@Unfolding Energy - sRNA 0.866923 kcal/mol@LB@@LB@Position - mRNA 243 -- 253@LB@Position - sRNA 42 -- 52@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 42 -- 48@LB@
137	0.02646	0.6177	b3807	cyaY	-4.99	0.375460	213 -- 221	38 -- 46	iron-dependent inhibitor of iron-sulfur cluster formation; frataxin; iron-binding and oxidizing protein	_____________212_______222\n_____________\|_________\|\n5'-UGA...ACAGU_________CGCCU...AAA-3'\n______________GAAUUUCAU\n______________\|\|\|\|\|\|\|\|\|\n______________CUUAAAGUA\n3'-UUU...UUCUC_________AAAAA...ACA-5'\n_____________\|_________\|\n_____________47________37\n	215 -- 221	38 -- 44	-7.89908 kcal/mol	1.90809 kcal/mol	1.00074 kcal/mol	212 222@LB@ \| \|@LB@5'-UGA...ACAGU CGCCU...AAA-3'@LB@ GAAUUUCAU@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUUAAAGUA@LB@3'-UUU...UUCUC AAAAA...ACA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -4.99 kcal/mol@LB@Hybridization Energy -7.89908 kcal/mol@LB@Unfolding Energy - mRNA 1.90809 kcal/mol@LB@Unfolding Energy - sRNA 1.00074 kcal/mol@LB@@LB@Position - mRNA 213 -- 221@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
68	0.01422	0.6177	b3826	yigL	-7.04	0.159921	44 -- 50	49 -- 55	pyridoxal phosphate phosphatase	_____________43______51\n_____________\|_______\|\n5'-GCA...AUCCU_______GAGGA...CGC-3'\n______________GUCGAAG\n______________\|\|\|:\|\|\|\n______________CAGUUUC\n3'-UUU...CCGGG_______UCCUU...ACA-5'\n_____________\|_______\|\n_____________56______48\n	44 -- 50	49 -- 55	-7.68974 kcal/mol	0.331193 kcal/mol	0.314364 kcal/mol	43 51@LB@ \| \|@LB@5'-GCA...AUCCU GAGGA...CGC-3'@LB@ GUCGAAG@LB@ \|\|\|:\|\|\|@LB@ CAGUUUC@LB@3'-UUU...CCGGG UCCUU...ACA-5'@LB@ \| \|@LB@ 56 48@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -7.68974 kcal/mol@LB@Unfolding Energy - mRNA 0.331193 kcal/mol@LB@Unfolding Energy - sRNA 0.314364 kcal/mol@LB@@LB@Position - mRNA 44 -- 50@LB@Position - sRNA 49 -- 55@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 49 -- 55@LB@
29	0.005664	0.6127	b3831	udp	-8.88	0.069383	184 -- 196	42 -- 54	uridine phosphorylase	_____________183___________197\n_____________\|_____________\|\n5'-AUC...CCGAU___C_________GUAUA...AGA-3'\n______________UCA_AGAGGAGUU\n______________\|\|\|_\|\|\|\|\|\|:\|\|\n______________AGU_UCUCCUUAA\n3'-UUU...CGGGC___U_________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________55____________41\n	190 -- 196	42 -- 48	-14.4874 kcal/mol	4.66075 kcal/mol	0.945538 kcal/mol	183 197@LB@ \| \|@LB@5'-AUC...CCGAU C GUAUA...AGA-3'@LB@ UCA AGAGGAGUU@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ AGU UCUCCUUAA@LB@3'-UUU...CGGGC U AGUAA...ACA-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -14.4874 kcal/mol@LB@Unfolding Energy - mRNA 4.66075 kcal/mol@LB@Unfolding Energy - sRNA 0.945538 kcal/mol@LB@@LB@Position - mRNA 184 -- 196@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 42 -- 48@LB@
147	0.02922	0.6177	b3836	tatA	-6.91	0.169904	186 -- 195	44 -- 53	TatABCE protein translocation system subunit	_____________185________196\n_____________\|__________\|\n5'-CUA...UCUAC__C_______CAUGU...GUG-3'\n______________CA_AGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\n______________GU_UCUCCUU\n3'-UUU...GGGCA__U_______AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	189 -- 195	44 -- 50	-10.6779 kcal/mol	2.84312 kcal/mol	0.927997 kcal/mol	185 196@LB@ \| \|@LB@5'-CUA...UCUAC C CAUGU...GUG-3'@LB@ CA AGAGGAA@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU UCUCCUU@LB@3'-UUU...GGGCA U AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -6.91 kcal/mol@LB@Hybridization Energy -10.6779 kcal/mol@LB@Unfolding Energy - mRNA 2.84312 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@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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