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
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@
172	0.007198	0.1466	b2395	yfeA	-7.88	0.166321	272 -- 292	49 -- 69	putative diguanylate cyclase	_____________271____________________293\n_____________\|______________________\|\n5'-ACC...GUACU__________UC____UU____UUCGCCAC-3'\n______________UAUUCAGCUA___CCG__UUAU\n______________\|\|\|\|\|\|\|\|:\|___\|\|\|__\|\|\|:\n______________AUAAGUCGGU___GGC__AAUG\n3'-AUU...AUUUU__________UUA___U_____CACUU...AUG-5'\n_____________\|______________________\|\n_____________70_____________________48\n	275 -- 281	60 -- 66	-16.2546 kcal/mol	2.18624 kcal/mol	6.21499 kcal/mol	271 293@LB@ \| \|@LB@5'-ACC...GUACU UC UU UUCGCCAC-3'@LB@ UAUUCAGCUA CCG UUAU@LB@ \|\|\|\|\|\|\|\|:\| \|\|\| \|\|\|:@LB@ AUAAGUCGGU GGC AAUG@LB@3'-AUU...AUUUU UUA U CACUU...AUG-5'@LB@ \| \|@LB@ 70 48@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -16.2546 kcal/mol@LB@Unfolding Energy - mRNA 2.18624 kcal/mol@LB@Unfolding Energy - sRNA 6.21499 kcal/mol@LB@@LB@Position - mRNA 272 -- 292@LB@Position - sRNA 49 -- 69@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 60 -- 66@LB@
179	0.007709	0.1511	b4111	proP	-8.76	0.100034	225 -- 232	49 -- 56	proline/glycine betaine transporter	_____________224______233\n_____________\|________\|\n5'-CAC...UAAAA________CCUUC...GUA-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	226 -- 232	49 -- 55	-10.6643 kcal/mol	1.60159 kcal/mol	0.317884 kcal/mol	224 233@LB@ \| \|@LB@5'-CAC...UAAAA CCUUC...GUA-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -10.6643 kcal/mol@LB@Unfolding Energy - mRNA 1.60159 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 225 -- 232@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 49 -- 55@LB@
183	0.007903	0.1519	b2725	hycA	-8.51	0.115738	229 -- 236	49 -- 56	regulator of the transcriptional regulator FhlA	_____________228______237\n_____________\|________\|\n5'-UUA...GAAAG________AUCGC...AGG-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	230 -- 236	49 -- 55	-10.9203 kcal/mol	2.09518 kcal/mol	0.317884 kcal/mol	228 237@LB@ \| \|@LB@5'-UUA...GAAAG AUCGC...AGG-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -10.9203 kcal/mol@LB@Unfolding Energy - mRNA 2.09518 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 229 -- 236@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 49 -- 55@LB@
73	0.001217	0.05856	b1702	ppsA	-8.47	0.118779	124 -- 132	50 -- 58	phosphoenolpyruvate synthase	_____________123_______133\n_____________\|_________\|\n5'-UAU...UUUUC_________AAUAU...AAA-3'\n______________AUCCGGUUA\n______________\|\|\|\|\|:\|\|\|\n______________UAGGCUAAU\n3'-AUU...CGGUU_________GCACU...AUG-5'\n_____________\|_________\|\n_____________59________49\n	126 -- 132	50 -- 56	-10.3571 kcal/mol	1.58803 kcal/mol	0.317553 kcal/mol	123 133@LB@ \| \|@LB@5'-UAU...UUUUC AAUAU...AAA-3'@LB@ AUCCGGUUA@LB@ \|\|\|\|\|:\|\|\|@LB@ UAGGCUAAU@LB@3'-AUU...CGGUU GCACU...AUG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -10.3571 kcal/mol@LB@Unfolding Energy - mRNA 1.58803 kcal/mol@LB@Unfolding Energy - sRNA 0.317553 kcal/mol@LB@@LB@Position - mRNA 124 -- 132@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 50 -- 56@LB@
143	0.005218	0.1284	b1922	fliA	-8.86	0.094137	133 -- 141	50 -- 58	RNA polymerase sigma 28 (sigma F) factor	_____________132_______142\n_____________\|_________\|\n5'-AGG...UAAUC_________AAAAC...UUC-3'\n______________GUCCGAUUA\n______________:\|\|\|\|\|\|\|\|\n______________UAGGCUAAU\n3'-AUU...CGGUU_________GCACU...AUG-5'\n_____________\|_________\|\n_____________59________49\n	135 -- 141	50 -- 56	-11.3914 kcal/mol	2.23267 kcal/mol	0.317553 kcal/mol	132 142@LB@ \| \|@LB@5'-AGG...UAAUC AAAAC...UUC-3'@LB@ GUCCGAUUA@LB@ :\|\|\|\|\|\|\|\|@LB@ UAGGCUAAU@LB@3'-AUU...CGGUU GCACU...AUG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -11.3914 kcal/mol@LB@Unfolding Energy - mRNA 2.23267 kcal/mol@LB@Unfolding Energy - sRNA 0.317553 kcal/mol@LB@@LB@Position - mRNA 133 -- 141@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 50 -- 56@LB@
148	0.00596	0.1406	b3426	glpD	-7.81	0.172743	213 -- 222	50 -- 59	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________212________223\n_____________\|__________\|\n5'-AAC...CCAAA__________UGAUA...AGG-3'\n______________GAUCUGAUUG\n______________:\|\|\|:\|\|\|\|:\n______________UUAGGCUAAU\n3'-AUU...UCGGU__________GCACU...AUG-5'\n_____________\|__________\|\n_____________60_________49\n	216 -- 222	50 -- 56	-9.79708 kcal/mol	1.6903 kcal/mol	0.31771 kcal/mol	212 223@LB@ \| \|@LB@5'-AAC...CCAAA UGAUA...AGG-3'@LB@ GAUCUGAUUG@LB@ :\|\|\|:\|\|\|\|:@LB@ UUAGGCUAAU@LB@3'-AUU...UCGGU GCACU...AUG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -9.79708 kcal/mol@LB@Unfolding Energy - mRNA 1.6903 kcal/mol@LB@Unfolding Energy - sRNA 0.31771 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
153	0.006198	0.1406	b3459	panM	-8.50	0.116540	144 -- 151	50 -- 57	PanD autocleavage accelerator panothenate synthesis	_____________143______152\n_____________\|________\|\n5'-AAA...AAGCC________AAUUA...UUG-3'\n______________UCCGAUUA\n______________\|\|\|\|\|\|\|\|\n______________AGGCUAAU\n3'-AUU...GGUUU________GCACU...AUG-5'\n_____________\|________\|\n_____________58_______49\n	145 -- 151	50 -- 56	-10.246 kcal/mol	1.44461 kcal/mol	0.317388 kcal/mol	143 152@LB@ \| \|@LB@5'-AAA...AAGCC AAUUA...UUG-3'@LB@ UCCGAUUA@LB@ \|\|\|\|\|\|\|\|@LB@ AGGCUAAU@LB@3'-AUU...GGUUU GCACU...AUG-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -10.246 kcal/mol@LB@Unfolding Energy - mRNA 1.44461 kcal/mol@LB@Unfolding Energy - sRNA 0.317388 kcal/mol@LB@@LB@Position - mRNA 144 -- 151@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 50 -- 56@LB@
174	0.007262	0.1466	b0473	htpG	-8.02	0.153160	10 -- 17	50 -- 57	protein refolding molecular co-chaperone Hsp90 Hsp70-dependent; heat-shock protein; ATPase	_____________9________18\n_____________\|________\|\n5'-UCA...GGCGU________GCGGC...GUG-3'\n______________UCCGGUUG\n______________\|\|\|\|:\|\|:\n______________AGGCUAAU\n3'-AUU...GGUUU________GCACU...AUG-5'\n_____________\|________\|\n_____________58_______49\n	11 -- 17	50 -- 56	-9.07782 kcal/mol	0.753256 kcal/mol	0.317388 kcal/mol	9 18@LB@ \| \|@LB@5'-UCA...GGCGU GCGGC...GUG-3'@LB@ UCCGGUUG@LB@ \|\|\|\|:\|\|:@LB@ AGGCUAAU@LB@3'-AUU...GGUUU GCACU...AUG-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -9.07782 kcal/mol@LB@Unfolding Energy - mRNA 0.753256 kcal/mol@LB@Unfolding Energy - sRNA 0.317388 kcal/mol@LB@@LB@Position - mRNA 10 -- 17@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 50 -- 56@LB@
167	0.00683	0.1439	b0387	yaiI	-9.54	0.061403	53 -- 70	51 -- 65	UPF0178 family protein	_____________52_________________71\n_____________\|__________________\|\n5'-CAC...UGCCG_______UAAAA______UUCUU...CAA-3'\n______________CAGCCAA_____CCGAUU\n______________\|\|\|\|\|\|\|_____\|\|\|\|\|\|\n______________GUCGGUU_____GGCUAA\n3'-AUU...UAUAA_______UA_________UGCAC...AUG-5'\n_____________\|__________________\|\n_____________66_________________50\n	53 -- 59	59 -- 65	-16.8495 kcal/mol	1.14267 kcal/mol	6.18987 kcal/mol	52 71@LB@ \| \|@LB@5'-CAC...UGCCG UAAAA UUCUU...CAA-3'@LB@ CAGCCAA CCGAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUCGGUU GGCUAA@LB@3'-AUU...UAUAA UA UGCAC...AUG-5'@LB@ \| \|@LB@ 66 50@LB@@LB@@LB@Energy -9.54 kcal/mol@LB@Hybridization Energy -16.8495 kcal/mol@LB@Unfolding Energy - mRNA 1.14267 kcal/mol@LB@Unfolding Energy - sRNA 6.18987 kcal/mol@LB@@LB@Position - mRNA 53 -- 70@LB@Position - sRNA 51 -- 65@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 59 -- 65@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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