Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
193	0.008653	0.1558	b1677	lpp	-9.16	0.078007	273 -- 298	53 -- 76	murein lipoprotein		_____________272________________________299\n_____________\|__________________________\|\n5'-UCA...GCAAC________CGA______GUCU_____CG-3'\n______________GCUAAAAU___UCAGCU____UCUGA\n______________\|\|\|\|\|\|\|\|___\|\|\|\|\|:____\|\|:\|\|\n______________CGAUUUUA___AGUCGG____AGGCU\n3'-AUU...CCCGC________UA_______UUU______AAUGC...AUG-5'\n_____________\|__________________________\|\n_____________77_________________________52\n	273 -- 279	70 -- 76	-19.09 kcal/mol	3.58418 kcal/mol	6.36489 kcal/mol	272 299@LB@ \| \|@LB@5'-UCA...GCAAC CGA GUCU CG-3'@LB@ GCUAAAAU UCAGCU UCUGA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|:\|\|@LB@ CGAUUUUA AGUCGG AGGCU@LB@3'-AUU...CCCGC UA UUU AAUGC...AUG-5'@LB@ \| \|@LB@ 77 52@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -19.09 kcal/mol@LB@Unfolding Energy - mRNA 3.58418 kcal/mol@LB@Unfolding Energy - sRNA 6.36489 kcal/mol@LB@@LB@Position - mRNA 273 -- 298@LB@Position - sRNA 53 -- 76@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 70 -- 76@LB@
36	0.0003681	0.03584	b1136	icd	-11.32	0.017792	275 -- 286	49 -- 60	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase		_____________274__________287\n_____________\|____________\|\n5'-GUA...CCUGA____________CCCUU...AAG-3'\n______________AAAUCCGAUUAU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UUUAGGCUAAUG\n3'-AUU...GUCGG____________CACUU...AUG-5'\n_____________\|____________\|\n_____________61___________48\n	280 -- 286	49 -- 55	-13.1162 kcal/mol	1.49253 kcal/mol	0.319946 kcal/mol	274 287@LB@ \| \|@LB@5'-GUA...CCUGA CCCUU...AAG-3'@LB@ AAAUCCGAUUAU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UUUAGGCUAAUG@LB@3'-AUU...GUCGG CACUU...AUG-5'@LB@ \| \|@LB@ 61 48@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -13.1162 kcal/mol@LB@Unfolding Energy - mRNA 1.49253 kcal/mol@LB@Unfolding Energy - sRNA 0.319946 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 49 -- 60@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 49 -- 55@LB@
26	0.0002109	0.02687	b4122	fumB	-13.50	0.002989	276 -- 286	47 -- 57	anaerobic class I fumarate hydratase (fumarase B)	b1612	_____________275_________287\n_____________\|___________\|\n5'-UCC...UCACU___________UAGCG...ACU-3'\n______________UCCGAUUACGU\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________AGGCUAAUGCA\n3'-AUU...GGUUU___________CUUCA...AUG-5'\n_____________\|___________\|\n_____________58__________46\n	280 -- 286	47 -- 53	-16.5827 kcal/mol	1.51899 kcal/mol	1.56839 kcal/mol	275 287@LB@ \| \|@LB@5'-UCC...UCACU UAGCG...ACU-3'@LB@ UCCGAUUACGU@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ AGGCUAAUGCA@LB@3'-AUU...GGUUU CUUCA...AUG-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -13.50 kcal/mol@LB@Hybridization Energy -16.5827 kcal/mol@LB@Unfolding Energy - mRNA 1.51899 kcal/mol@LB@Unfolding Energy - sRNA 1.56839 kcal/mol@LB@@LB@Position - mRNA 276 -- 286@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 47 -- 53@LB@
15	5.569e-05	0.01183	b1761	gdhA	-12.26	0.008568	280 -- 294	40 -- 56	glutamate dehydrogenase NADP-specific		_____________279_______________295\n_____________\|_________________\|\n5'-UAA...GCAAG___UU____________UGACCA-3'\n______________CCG____CGUGAAGUAA\n______________\|\|\|____\|\|\|\|\|\|\|\|\|\|\n______________GGC____GCACUUCAUU\n3'-AUU...GUUUA___UAAU__________UUCCA...AUG-5'\n_____________\|_________________\|\n_____________57________________39\n	288 -- 294	40 -- 46	-17.1153 kcal/mol	1.5283 kcal/mol	3.34823 kcal/mol	279 295@LB@ \| \|@LB@5'-UAA...GCAAG UU UGACCA-3'@LB@ CCG CGUGAAGUAA@LB@ \|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ GGC GCACUUCAUU@LB@3'-AUU...GUUUA UAAU UUCCA...AUG-5'@LB@ \| \|@LB@ 57 39@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -17.1153 kcal/mol@LB@Unfolding Energy - mRNA 1.5283 kcal/mol@LB@Unfolding Energy - sRNA 3.34823 kcal/mol@LB@@LB@Position - mRNA 280 -- 294@LB@Position - sRNA 40 -- 56@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 40 -- 46@LB@
87	0.00233	0.09349	b2522	sseB	-8.85	0.094489	280 -- 288	1 -- 9	rhodanase-like enzyme sulfur transfer from thiosulfate		_____________279_______289\n_____________\|_________\|\n5'-GGU...UUUCC_________UGGAA...CCG-3'\n______________GUACUCUAC\n______________\|\|\|\|:\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	282 -- 288	1 -- 7	-12.3435 kcal/mol	1.38525 kcal/mol	2.12872 kcal/mol	279 289@LB@ \| \|@LB@5'-GGU...UUUCC UGGAA...CCG-3'@LB@ GUACUCUAC@LB@ \|\|\|\|:\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.3435 kcal/mol@LB@Unfolding Energy - mRNA 1.38525 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 280 -- 288@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 1 -- 7@LB@
107	0.003396	0.1101	b3871	typA	-9.79	0.052081	283 -- 294	47 -- 59	GTP-binding protein		_____________282___________295\n_____________\|_____________\|\n5'-UGC...CCAAC_____________UCGACU-3'\n______________AAUCCGGU_ACGU\n______________\|\|\|\|\|\|:\|_\|\|\|\|\n______________UUAGGCUA_UGCA\n3'-AUU...UCGGU________A____CUUCA...AUG-5'\n_____________\|_____________\|\n_____________60____________46\n	284 -- 290	52 -- 58	-13.0383 kcal/mol	1.68034 kcal/mol	1.56852 kcal/mol	282 295@LB@ \| \|@LB@5'-UGC...CCAAC UCGACU-3'@LB@ AAUCCGGU ACGU@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ UUAGGCUA UGCA@LB@3'-AUU...UCGGU A CUUCA...AUG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -9.79 kcal/mol@LB@Hybridization Energy -13.0383 kcal/mol@LB@Unfolding Energy - mRNA 1.68034 kcal/mol@LB@Unfolding Energy - sRNA 1.56852 kcal/mol@LB@@LB@Position - mRNA 283 -- 294@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 52 -- 58@LB@
137	0.004974	0.127	b0092	ddlB	-6.99	0.263821	283 -- 297	43 -- 56	D-alanine:D-alanine ligase		_____________282_____________298\n_____________\|_______________\|\n5'-UUC...GUUAG____AC_________GCG-3'\n______________CCGG__UGCGUGAAG\n______________\|\|\|:__\|:\|\|\|\|\|\|\|\n______________GGCU__AUGCACUUC\n3'-AUU...GUUUA____A__________AUUUU...AUG-5'\n_____________\|_______________\|\n_____________57______________42\n	291 -- 297	43 -- 49	-17.3937 kcal/mol	7.14584 kcal/mol	3.27327 kcal/mol	282 298@LB@ \| \|@LB@5'-UUC...GUUAG AC GCG-3'@LB@ CCGG UGCGUGAAG@LB@ \|\|\|: \|:\|\|\|\|\|\|\|@LB@ GGCU AUGCACUUC@LB@3'-AUU...GUUUA A AUUUU...AUG-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -17.3937 kcal/mol@LB@Unfolding Energy - mRNA 7.14584 kcal/mol@LB@Unfolding Energy - sRNA 3.27327 kcal/mol@LB@@LB@Position - mRNA 283 -- 297@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 43 -- 49@LB@
171	0.00718	0.1466	b1708	nlpC	-9.44	0.065343	288 -- 298	49 -- 59	putative C40 clan peptidase lipoprotein		_____________287_________299\n_____________\|___________\|\n5'-AAA...UUUCU___________CG-3'\n______________GAUUCGAUUAC\n______________:\|\|:\|\|\|\|\|\|\|\n______________UUAGGCUAAUG\n3'-AUU...UCGGU___________CACUU...AUG-5'\n_____________\|___________\|\n_____________60__________48\n	292 -- 298	49 -- 55	-11.5278 kcal/mol	1.77565 kcal/mol	0.318405 kcal/mol	287 299@LB@ \| \|@LB@5'-AAA...UUUCU CG-3'@LB@ GAUUCGAUUAC@LB@ :\|\|:\|\|\|\|\|\|\|@LB@ UUAGGCUAAUG@LB@3'-AUU...UCGGU CACUU...AUG-5'@LB@ \| \|@LB@ 60 48@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -11.5278 kcal/mol@LB@Unfolding Energy - mRNA 1.77565 kcal/mol@LB@Unfolding Energy - sRNA 0.318405 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 49 -- 59@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 49 -- 55@LB@
44	0.000471	0.03766	b3624	waaZ	-7.10	0.250129	289 -- 295	1 -- 7	lipopolysaccharide KdoIII transferase; lipopolysaccharide core biosynthesis protein		_____________288_____296\n_____________\|_______\|\n5'-AGA...UUCGG_______AUCGC-3'\n______________GCCCUAC\n______________:\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	289 -- 295	1 -- 7	-11.6335 kcal/mol	2.52016 kcal/mol	2.03949 kcal/mol	288 296@LB@ \| \|@LB@5'-AGA...UUCGG AUCGC-3'@LB@ GCCCUAC@LB@ :\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -11.6335 kcal/mol@LB@Unfolding Energy - mRNA 2.52016 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 1 -- 7@LB@
158	0.00634	0.1412	b3598	yibI	-10.19	0.039756	289 -- 298	49 -- 58	DUF3302 family inner membrane protein	b3587	_____________288________299\n_____________\|__________\|\n5'-CGU...CCCUU__________CA-3'\n______________AUCUGAUUGC\n______________\|\|\|:\|\|\|\|:\|\n______________UAGGCUAAUG\n3'-AUU...CGGUU__________CACUU...AUG-5'\n_____________\|__________\|\n_____________59_________48\n	292 -- 298	49 -- 55	-10.9433 kcal/mol	0.440755 kcal/mol	0.318367 kcal/mol	288 299@LB@ \| \|@LB@5'-CGU...CCCUU CA-3'@LB@ AUCUGAUUGC@LB@ \|\|\|:\|\|\|\|:\|@LB@ UAGGCUAAUG@LB@3'-AUU...CGGUU CACUU...AUG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -10.9433 kcal/mol@LB@Unfolding Energy - mRNA 0.440755 kcal/mol@LB@Unfolding Energy - sRNA 0.318367 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 49 -- 55@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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