Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
172	0.03064	0.5559	b1542	ydfI	-13.08	0.030437	273 -- 290	69 -- 86	putative NAD-dependent D-mannonate oxidoreductase	_____________272________________291\n_____________\|__________________\|\n5'-CUC...GAAUU______UUA_________GCAUU...ACC-3'\n______________GUUCAU___GGCUUUGGU\n______________\|\|\|\|\|:___\|\|\|\|\|\|:\|\|\n______________CAAGUG___CCGAAAUCA\n3'-CGC...GUUUU______CAA_________AUAAG...AAG-5'\n_____________\|__________________\|\n_____________87_________________68\n	284 -- 290	69 -- 75	-19.6529 kcal/mol	6.00837 kcal/mol	0.568509 kcal/mol	272 291@LB@ \| \|@LB@5'-CUC...GAAUU UUA GCAUU...ACC-3'@LB@ GUUCAU GGCUUUGGU@LB@ \|\|\|\|\|: \|\|\|\|\|\|:\|\|@LB@ CAAGUG CCGAAAUCA@LB@3'-CGC...GUUUU CAA AUAAG...AAG-5'@LB@ \| \|@LB@ 87 68@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -19.6529 kcal/mol@LB@Unfolding Energy - mRNA 6.00837 kcal/mol@LB@Unfolding Energy - sRNA 0.568509 kcal/mol@LB@@LB@Position - mRNA 273 -- 290@LB@Position - sRNA 69 -- 86@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@LB@
30	0.005373	0.5385	b1624	ydgJ	-10.76	0.078067	229 -- 247	61 -- 79	putative oxidoreductase	_____________228_________________248\n_____________\|___________________\|\n5'-GUA...GUUGA____G_A_______G____CAAAA...CGG-3'\n______________UUGG_U_UGGUUAU_CGAG\n______________\|\|\|\|_\|_\|:\|\|\|\|\|_\|\|\|\|\n______________AACC_A_AUCAAUA_GCUC\n3'-CGC...AGUGC____G_A_______A____AACUC...AAG-5'\n_____________\|___________________\|\n_____________80__________________60\n	236 -- 242	66 -- 72	-16.8363 kcal/mol	5.27817 kcal/mol	0.798019 kcal/mol	228 248@LB@ \| \|@LB@5'-GUA...GUUGA G A G CAAAA...CGG-3'@LB@ UUGG U UGGUUAU CGAG@LB@ \|\|\|\| \| \|:\|\|\|\|\| \|\|\|\|@LB@ AACC A AUCAAUA GCUC@LB@3'-CGC...AGUGC G A A AACUC...AAG-5'@LB@ \| \|@LB@ 80 60@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -16.8363 kcal/mol@LB@Unfolding Energy - mRNA 5.27817 kcal/mol@LB@Unfolding Energy - sRNA 0.798019 kcal/mol@LB@@LB@Position - mRNA 229 -- 247@LB@Position - sRNA 61 -- 79@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 66 -- 72@LB@
155	0.02668	0.5559	b1625	cnu	-8.12	0.218326	240 -- 246	81 -- 87	nucleoid-associated oriC-binding protein; H-NS and StpA stabilizing factor	_____________239_____247\n_____________\|_______\|\n5'-UUU...AAAUC_______UCGAA...AUC-3'\n______________AGUUCAC\n______________\|\|\|\|\|\|\|\n______________UCAAGUG\n3'-CGC...CGUUU_______CAACC...AAG-5'\n_____________\|_______\|\n_____________88______80\n	240 -- 246	81 -- 87	-9.1905 kcal/mol	0.576286 kcal/mol	0.494577 kcal/mol	239 247@LB@ \| \|@LB@5'-UUU...AAAUC UCGAA...AUC-3'@LB@ AGUUCAC@LB@ \|\|\|\|\|\|\|@LB@ UCAAGUG@LB@3'-CGC...CGUUU CAACC...AAG-5'@LB@ \| \|@LB@ 88 80@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.1905 kcal/mol@LB@Unfolding Energy - mRNA 0.576286 kcal/mol@LB@Unfolding Energy - sRNA 0.494577 kcal/mol@LB@@LB@Position - mRNA 240 -- 246@LB@Position - sRNA 81 -- 87@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 81 -- 87@LB@
17	0.003067	0.5385	b1628	rsxB	-11.62	0.055094	175 -- 198	58 -- 77	SoxR iron-sulfur cluster reduction factor component; putative iron-sulfur protein	_____________174______________________199\n_____________\|________________________\|\n5'-CAC...UUAUG_________G_____GUGA_____UAAUG...ACG-3'\n______________GGCUUUAGU_GUUUG____AGUUG\n______________\|\|\|\|\|\|\|\|\|_:\|\|:\|____\|\|\|\|\|\n______________CCGAAAUCA_UAAGC____UCAAC\n3'-CGC...UGCAA_________A______________UCUUU...AAG-5'\n_____________\|________________________\|\n_____________78_______________________57\n	177 -- 183	69 -- 75	-20.3316 kcal/mol	7.50919 kcal/mol	1.19974 kcal/mol	174 199@LB@ \| \|@LB@5'-CAC...UUAUG G GUGA UAAUG...ACG-3'@LB@ GGCUUUAGU GUUUG AGUUG@LB@ \|\|\|\|\|\|\|\|\| :\|\|:\| \|\|\|\|\|@LB@ CCGAAAUCA UAAGC UCAAC@LB@3'-CGC...UGCAA A UCUUU...AAG-5'@LB@ \| \|@LB@ 78 57@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -20.3316 kcal/mol@LB@Unfolding Energy - mRNA 7.50919 kcal/mol@LB@Unfolding Energy - sRNA 1.19974 kcal/mol@LB@@LB@Position - mRNA 175 -- 198@LB@Position - sRNA 58 -- 77@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 69 -- 75@LB@
170	0.03041	0.5559	b1629	rsxC	-10.04	0.103937	197 -- 215	64 -- 83	SoxR iron-sulfur cluster reduction factor component; putative membrane-associated NADH oxidoreductase of electron transport complex	_____________196__________________216\n_____________\|____________________\|\n5'-UCA...UGGAA___CAU_____A________UCUGC...CCC-3'\n______________CAC____GCUU_AGUUAUUC\n______________\|\|\|____\|\|\|\|_\|\|\|\|\|\|\|\|\n______________GUG____CGAA_UCAAUAAG\n3'-CGC...UUCAA___CAAC____A________CUCAA...AAG-5'\n_____________\|____________________\|\n_____________84___________________63\n	209 -- 215	64 -- 70	-13.7112 kcal/mol	3.10702 kcal/mol	0.560651 kcal/mol	196 216@LB@ \| \|@LB@5'-UCA...UGGAA CAU A UCUGC...CCC-3'@LB@ CAC GCUU AGUUAUUC@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUG CGAA UCAAUAAG@LB@3'-CGC...UUCAA CAAC A CUCAA...AAG-5'@LB@ \| \|@LB@ 84 63@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -13.7112 kcal/mol@LB@Unfolding Energy - mRNA 3.10702 kcal/mol@LB@Unfolding Energy - sRNA 0.560651 kcal/mol@LB@@LB@Position - mRNA 197 -- 215@LB@Position - sRNA 64 -- 83@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 64 -- 70@LB@
39	0.007274	0.5385	b1636	pdxY	-13.08	0.030384	230 -- 254	60 -- 84	pyridoxamine kinase	_____________229_______________________255\n_____________\|_________________________\|\n5'-UAU...CAGUC________U__A____C__G_____AACAG...UCU-3'\n______________UCACGUUG_UU_UGGU_AU_CGGGU\n______________\|\|\|\|\|\|\|\|_:\|_\|:\|\|_\|\|_\|\|:\|\|\n______________AGUGCAAC_GA_AUCA_UA_GCUCA\n3'-CGC...UUUCA________C__A____A__A_____ACUCU...AAG-5'\n_____________\|_________________________\|\n_____________85________________________59\n	231 -- 237	77 -- 83	-19.8659 kcal/mol	5.09201 kcal/mol	1.69371 kcal/mol	229 255@LB@ \| \|@LB@5'-UAU...CAGUC U A C G AACAG...UCU-3'@LB@ UCACGUUG UU UGGU AU CGGGU@LB@ \|\|\|\|\|\|\|\| :\| \|:\|\| \|\| \|\|:\|\|@LB@ AGUGCAAC GA AUCA UA GCUCA@LB@3'-CGC...UUUCA C A A A ACUCU...AAG-5'@LB@ \| \|@LB@ 85 59@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -19.8659 kcal/mol@LB@Unfolding Energy - mRNA 5.09201 kcal/mol@LB@Unfolding Energy - sRNA 1.69371 kcal/mol@LB@@LB@Position - mRNA 230 -- 254@LB@Position - sRNA 60 -- 84@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 77 -- 83@LB@
66	0.01284	0.5385	b1645	ydhK	-10.57	0.084210	155 -- 164	75 -- 84	putative efflux protein (PET) component of YdhJK efflux pump	_____________154________165\n_____________\|__________\|\n5'-CAG...CGAUG__________GUCGG...UGG-3'\n______________UCACGUUGGU\n______________\|\|\|\|\|\|\|\|\|:\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	158 -- 164	75 -- 81	-15.7281 kcal/mol	4.6508 kcal/mol	0.505918 kcal/mol	154 165@LB@ \| \|@LB@5'-CAG...CGAUG GUCGG...UGG-3'@LB@ UCACGUUGGU@LB@ \|\|\|\|\|\|\|\|\|:@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -15.7281 kcal/mol@LB@Unfolding Energy - mRNA 4.6508 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 155 -- 164@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 75 -- 81@LB@
139	0.02326	0.5385	b1651	gloA	-10.25	0.095619	225 -- 233	75 -- 83	glyoxalase I Ni-dependent	_____________224_______234\n_____________\|_________\|\n5'-UGG...UGCUG_________GAUUU...AAA-3'\n______________CGCGUUGGC\n______________\|:\|\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	227 -- 233	75 -- 81	-16.4206 kcal/mol	5.67498 kcal/mol	0.492259 kcal/mol	224 234@LB@ \| \|@LB@5'-UGG...UGCUG GAUUU...AAA-3'@LB@ CGCGUUGGC@LB@ \|:\|\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -16.4206 kcal/mol@LB@Unfolding Energy - mRNA 5.67498 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 225 -- 233@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 75 -- 81@LB@
9	0.0016	0.5385	b1709	btuD	-9.25	0.141890	185 -- 194	75 -- 84	vitamin B12 ABC transporter ATPase	_____________184________195\n_____________\|__________\|\n5'-GCA...UAAAC_G________AAAAU...GGC-3'\n______________U_GCGUUGGC\n______________\|_:\|\|\|\|\|\|\|\n______________A_UGCAACCG\n3'-CGC...UUUCA_G________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	188 -- 194	75 -- 81	-15.1998 kcal/mol	5.44246 kcal/mol	0.505918 kcal/mol	184 195@LB@ \| \|@LB@5'-GCA...UAAAC G AAAAU...GGC-3'@LB@ U GCGUUGGC@LB@ \| :\|\|\|\|\|\|\|@LB@ A UGCAACCG@LB@3'-CGC...UUUCA G AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -15.1998 kcal/mol@LB@Unfolding Energy - mRNA 5.44246 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 75 -- 81@LB@
131	0.02244	0.5385	b1713	pheT	-10.81	0.076409	64 -- 80	73 -- 89	phenylalanine tRNA synthetase beta subunit	_____________63________________81\n_____________\|_________________\|\n5'-CUG...ACCCG_________UC______CGCCU...ACG-3'\n______________GAAGUUUAC__UGGUUU\n______________:\|\|\|\|\|:\|\|__\|\|\|:\|\|\n______________UUUCAAGUG__ACCGAA\n3'-CGC...GGCGU_________CA______AUCAA...AAG-5'\n_____________\|_________________\|\n_____________90________________72\n	66 -- 72	81 -- 87	-14.6363 kcal/mol	3.30516 kcal/mol	0.517627 kcal/mol	63 81@LB@ \| \|@LB@5'-CUG...ACCCG UC CGCCU...ACG-3'@LB@ GAAGUUUAC UGGUUU@LB@ :\|\|\|\|\|:\|\| \|\|\|:\|\|@LB@ UUUCAAGUG ACCGAA@LB@3'-CGC...GGCGU CA AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -10.81 kcal/mol@LB@Hybridization Energy -14.6363 kcal/mol@LB@Unfolding Energy - mRNA 3.30516 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 64 -- 80@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 81 -- 87@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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service.

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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