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
74	0.001232	0.05856	b3139	agaC	-9.25	0.073815	213 -- 219	1 -- 7	N-acetylgalactosamine-specific enzyme IIC component of PTS	_____________212_____220\n_____________\|_______\|\n5'-AAC...AAAUA_______UUCAG...CGA-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	213 -- 219	1 -- 7	-11.8132 kcal/mol	0.545455 kcal/mol	2.03949 kcal/mol	212 220@LB@ \| \|@LB@5'-AAC...AAAUA UUCAG...CGA-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -11.8132 kcal/mol@LB@Unfolding Energy - mRNA 0.545455 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 213 -- 219@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 1 -- 7@LB@
52	0.0006736	0.04557	b3964	yijD	-9.23	0.074829	177 -- 192	43 -- 57	DUF1422 family inner membrane protein	_____________176______________193\n_____________\|________________\|\n5'-ACU...AUUAU_____GAA________GACGA...UGC-3'\n______________UCCGG___AUGUGAAG\n______________\|\|\|\|:___\|:\|\|\|\|\|\|\n______________AGGCU___UGCACUUC\n3'-AUU...GGUUU_____AA_________AUUUU...AUG-5'\n_____________\|________________\|\n_____________58_______________42\n	186 -- 192	43 -- 49	-16.7307 kcal/mol	4.24116 kcal/mol	3.27382 kcal/mol	176 193@LB@ \| \|@LB@5'-ACU...AUUAU GAA GACGA...UGC-3'@LB@ UCCGG AUGUGAAG@LB@ \|\|\|\|: \|:\|\|\|\|\|\|@LB@ AGGCU UGCACUUC@LB@3'-AUU...GGUUU AA AUUUU...AUG-5'@LB@ \| \|@LB@ 58 42@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -16.7307 kcal/mol@LB@Unfolding Energy - mRNA 4.24116 kcal/mol@LB@Unfolding Energy - sRNA 3.27382 kcal/mol@LB@@LB@Position - mRNA 177 -- 192@LB@Position - sRNA 43 -- 57@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 43 -- 49@LB@
111	0.003555	0.1127	b2938	speA	-9.18	0.077057	36 -- 48	46 -- 58	biosynthetic arginine decarboxylase PLP-binding	_____________35____________49\n_____________\|_____________\|\n5'-GUU...CUUAC_____________CUUAA...GCA-3'\n______________GUUCGGUUAUGUG\n______________:\|:\|\|:\|\|\|:\|\|\|\n______________UAGGCUAAUGCAC\n3'-AUU...CGGUU_____________UUCAU...AUG-5'\n_____________\|_____________\|\n_____________59____________45\n	42 -- 48	46 -- 52	-14.853 kcal/mol	3.8258 kcal/mol	1.8625 kcal/mol	35 49@LB@ \| \|@LB@5'-GUU...CUUAC CUUAA...GCA-3'@LB@ GUUCGGUUAUGUG@LB@ :\|:\|\|:\|\|\|:\|\|\|@LB@ UAGGCUAAUGCAC@LB@3'-AUU...CGGUU UUCAU...AUG-5'@LB@ \| \|@LB@ 59 45@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -14.853 kcal/mol@LB@Unfolding Energy - mRNA 3.8258 kcal/mol@LB@Unfolding Energy - sRNA 1.8625 kcal/mol@LB@@LB@Position - mRNA 36 -- 48@LB@Position - sRNA 46 -- 58@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 46 -- 52@LB@
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@
30	0.0002612	0.03063	b3789	rffH	-9.15	0.078548	244 -- 254	48 -- 58	glucose-1-phosphate thymidylyltransferase	_____________243_________255\n_____________\|___________\|\n5'-GGC...AUUGC___________CGCGG...UGA-3'\n______________AUCCGAUUACG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UAGGCUAAUGC\n3'-AUU...CGGUU___________ACUUC...AUG-5'\n_____________\|___________\|\n_____________59__________47\n	248 -- 254	48 -- 54	-15.7126 kcal/mol	4.98099 kcal/mol	1.55987 kcal/mol	243 255@LB@ \| \|@LB@5'-GGC...AUUGC CGCGG...UGA-3'@LB@ AUCCGAUUACG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UAGGCUAAUGC@LB@3'-AUU...CGGUU ACUUC...AUG-5'@LB@ \| \|@LB@ 59 47@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -15.7126 kcal/mol@LB@Unfolding Energy - mRNA 4.98099 kcal/mol@LB@Unfolding Energy - sRNA 1.55987 kcal/mol@LB@@LB@Position - mRNA 244 -- 254@LB@Position - sRNA 48 -- 58@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 48 -- 54@LB@
197	0.00873	0.1558	b2324	mnmC	-9.11	0.080832	111 -- 120	52 -- 61	fused 5-methylaminomethyl-2-thiouridine-forming enzyme methyltransferase and FAD-dependent demodification enzyme	_____________110________121\n_____________\|__________\|\n5'-GCU...CCGAA__________CAGCC...ACG-3'\n______________CAAGUCCGAU\n______________\|\|\|:\|\|\|\|\|\|\n______________GUUUAGGCUA\n3'-AUU...AGUCG__________AUGCA...AUG-5'\n_____________\|__________\|\n_____________62_________51\n	114 -- 120	52 -- 58	-12.6788 kcal/mol	1.38997 kcal/mol	2.20422 kcal/mol	110 121@LB@ \| \|@LB@5'-GCU...CCGAA CAGCC...ACG-3'@LB@ CAAGUCCGAU@LB@ \|\|\|:\|\|\|\|\|\|@LB@ GUUUAGGCUA@LB@3'-AUU...AGUCG AUGCA...AUG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -9.11 kcal/mol@LB@Hybridization Energy -12.6788 kcal/mol@LB@Unfolding Energy - mRNA 1.38997 kcal/mol@LB@Unfolding Energy - sRNA 2.20422 kcal/mol@LB@@LB@Position - mRNA 111 -- 120@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 52 -- 58@LB@
135	0.004796	0.125	b3634	coaD	-9.06	0.083023	69 -- 85	49 -- 66	pantetheine-phosphate adenylyltransferase	_____________68_________________86\n_____________\|__________________\|\n5'-GGA...UUUAC________CG________CGUAG...UUC-3'\n______________UCA_CCGA__CCGAUUAC\n______________\|\|\|_\|\|:\|__\|\|\|\|\|\|\|\|\n______________AGU_GGUU__GGCUAAUG\n3'-AUU...UUAUA___C____UA________CACUU...AUG-5'\n_____________\|__________________\|\n_____________67_________________48\n	79 -- 85	49 -- 55	-17.7938 kcal/mol	2.54845 kcal/mol	6.20469 kcal/mol	68 86@LB@ \| \|@LB@5'-GGA...UUUAC CG CGUAG...UUC-3'@LB@ UCA CCGA CCGAUUAC@LB@ \|\|\| \|\|:\| \|\|\|\|\|\|\|\|@LB@ AGU GGUU GGCUAAUG@LB@3'-AUU...UUAUA C UA CACUU...AUG-5'@LB@ \| \|@LB@ 67 48@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -17.7938 kcal/mol@LB@Unfolding Energy - mRNA 2.54845 kcal/mol@LB@Unfolding Energy - sRNA 6.20469 kcal/mol@LB@@LB@Position - mRNA 69 -- 85@LB@Position - sRNA 49 -- 66@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 49 -- 55@LB@
93	0.002634	0.09947	b2202	napC	-9.04	0.084220	177 -- 197	34 -- 54	quinol dehydrogenase electron source for NapAB	_____________176___________________198\n_____________\|_____________________\|\n5'-ACG...CAAAA_______G___A_________AUUAU...GUU-3'\n______________GGUUACG_GAA_UAAGAGGUU\n______________\|:\|\|\|\|\|_\|\|\|_\|\|\|:\|\|\|\|:\n______________CUAAUGC_CUU_AUUUUCCAG\n3'-AUU...UUAGG_______A___C_________ACUUU...AUG-5'\n_____________\|_____________________\|\n_____________55____________________33\n	177 -- 183	48 -- 54	-21.2793 kcal/mol	4.43682 kcal/mol	7.71857 kcal/mol	176 198@LB@ \| \|@LB@5'-ACG...CAAAA G A AUUAU...GUU-3'@LB@ GGUUACG GAA UAAGAGGUU@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|:\|\|\|\|:@LB@ CUAAUGC CUU AUUUUCCAG@LB@3'-AUU...UUAGG A C ACUUU...AUG-5'@LB@ \| \|@LB@ 55 33@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -21.2793 kcal/mol@LB@Unfolding Energy - mRNA 4.43682 kcal/mol@LB@Unfolding Energy - sRNA 7.71857 kcal/mol@LB@@LB@Position - mRNA 177 -- 197@LB@Position - sRNA 34 -- 54@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 48 -- 54@LB@
34	0.0003499	0.03519	b0333	prpC	-9.01	0.085770	169 -- 175	1 -- 7	2-methylcitrate synthase	_____________168_____176\n_____________\|_______\|\n5'-ACU...UCUCG_______AAAUG...GCA-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	169 -- 175	1 -- 7	-11.7504 kcal/mol	0.722985 kcal/mol	2.03949 kcal/mol	168 176@LB@ \| \|@LB@5'-ACU...UCUCG AAAUG...GCA-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -11.7504 kcal/mol@LB@Unfolding Energy - mRNA 0.722985 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 169 -- 175@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 1 -- 7@LB@
7	1.5e-05	0.00754	b0720	gltA	-8.97	0.087950	70 -- 79	4 -- 13	citrate synthase	_____________69_________80\n_____________\|__________\|\n5'-CGG...CAGAG__________AGGUU...GUA-3'\n______________CUCUGUACCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________GAGACAUGGG\n3'-AUU...GAAUG__________AUG-5'\n_____________\|__________\|\n_____________14_________3\n	73 -- 79	4 -- 10	-18.8657 kcal/mol	4.79377 kcal/mol	5.12835 kcal/mol	69 80@LB@ \| \|@LB@5'-CGG...CAGAG AGGUU...GUA-3'@LB@ CUCUGUACCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GAGACAUGGG@LB@3'-AUU...GAAUG AUG-5'@LB@ \| \|@LB@ 14 3@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -18.8657 kcal/mol@LB@Unfolding Energy - mRNA 4.79377 kcal/mol@LB@Unfolding Energy - sRNA 5.12835 kcal/mol@LB@@LB@Position - mRNA 70 -- 79@LB@Position - sRNA 4 -- 13@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 4 -- 10@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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