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
125	0.004186	0.1178	b0781	moaA	-8.90	0.091954	79 -- 99	4 -- 23	molybdopterin biosynthesis protein A	_____________78____________________100\n_____________\|_____________________\|\n5'-ACG...CACUA____C___A_______C____GGGUC...CGG-3'\n______________AACA_UCU_GCCUCUG_ACCU\n______________\|\|\|\|_\|\|\|_:\|\|\|\|\|\|_\|\|\|:\n______________UUGU_AGA_UGGAGAC_UGGG\n3'-AUU...CUAUC________A_______A____AUG-5'\n_____________\|_____________________\|\n_____________24____________________3\n	88 -- 94	9 -- 15	-21.7522 kcal/mol	4.86496 kcal/mol	8.01134 kcal/mol	78 100@LB@ \| \|@LB@5'-ACG...CACUA C A C GGGUC...CGG-3'@LB@ AACA UCU GCCUCUG ACCU@LB@ \|\|\|\| \|\|\| :\|\|\|\|\|\| \|\|\|:@LB@ UUGU AGA UGGAGAC UGGG@LB@3'-AUU...CUAUC A A AUG-5'@LB@ \| \|@LB@ 24 3@LB@@LB@@LB@Energy -8.90 kcal/mol@LB@Hybridization Energy -21.7522 kcal/mol@LB@Unfolding Energy - mRNA 4.86496 kcal/mol@LB@Unfolding Energy - sRNA 8.01134 kcal/mol@LB@@LB@Position - mRNA 79 -- 99@LB@Position - sRNA 4 -- 23@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 9 -- 15@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@
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@
164	0.006623	0.1421	b2278	nuoL	-8.77	0.099276	203 -- 221	5 -- 24	NADH:ubiquinone oxidoreductase membrane subunit L	_____________202___________________222\n_____________\|_____________________\|\n5'-GGU...CGGAU______G________A_____AUUAU...UCG-3'\n______________GAACAU_CUUGCCUU___ACC\n______________\|\|\|\|\|\|_\|\|\|:\|\|\|:___\|\|\|\n______________CUUGUA_GAAUGGAG___UGG\n3'-AUU...UCUAU_______________ACA___GAUG-5'\n_____________\|_____________________\|\n_____________25____________________4\n	211 -- 217	11 -- 17	-20.7037 kcal/mol	3.94864 kcal/mol	8.01095 kcal/mol	202 222@LB@ \| \|@LB@5'-GGU...CGGAU G A AUUAU...UCG-3'@LB@ GAACAU CUUGCCUU ACC@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|: \|\|\|@LB@ CUUGUA GAAUGGAG UGG@LB@3'-AUU...UCUAU ACA GAUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -8.77 kcal/mol@LB@Hybridization Energy -20.7037 kcal/mol@LB@Unfolding Energy - mRNA 3.94864 kcal/mol@LB@Unfolding Energy - sRNA 8.01095 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@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@
35	0.0003501	0.03519	b2700	pncC	-8.73	0.102058	11 -- 28	20 -- 37	nicotinamide-nucleotide amidohydrolase; NMN amidohydrolase	_____________10_________________29\n_____________\|__________________\|\n5'-ACG...AUGGC_______C__U_______AGCCG...GUU-3'\n______________GGUCUGG_AG_UAGGACA\n______________\|\|\|\|\|\|:_\|\|_\|\|\|:\|\|\|\n______________CCAGACU_UC_AUCUUGU\n3'-AUU...AUUUU_______U__U_______AGAAU...AUG-5'\n_____________\|__________________\|\n_____________38_________________19\n	22 -- 28	20 -- 26	-19.0339 kcal/mol	5.51285 kcal/mol	4.72108 kcal/mol	10 29@LB@ \| \|@LB@5'-ACG...AUGGC C U AGCCG...GUU-3'@LB@ GGUCUGG AG UAGGACA@LB@ \|\|\|\|\|\|: \|\| \|\|\|:\|\|\|@LB@ CCAGACU UC AUCUUGU@LB@3'-AUU...AUUUU U U AGAAU...AUG-5'@LB@ \| \|@LB@ 38 19@LB@@LB@@LB@Energy -8.73 kcal/mol@LB@Hybridization Energy -19.0339 kcal/mol@LB@Unfolding Energy - mRNA 5.51285 kcal/mol@LB@Unfolding Energy - sRNA 4.72108 kcal/mol@LB@@LB@Position - mRNA 11 -- 28@LB@Position - sRNA 20 -- 37@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 20 -- 26@LB@
186	0.008252	0.1556	b2026	hisI	-8.65	0.106637	17 -- 26	42 -- 51	phosphoribosyl-AMP cyclohydrolase and phosphoribosyl-ATP pyrophosphatase	_____________16_________27\n_____________\|__________\|\n5'-GAA...AAAAG__________UUGCC...UGC-3'\n______________UGCGUGAAGU\n______________\|:\|\|\|\|\|\|\|\|\n______________AUGCACUUCA\n3'-AUU...GGCUA__________UUUUC...AUG-5'\n_____________\|__________\|\n_____________52_________41\n	20 -- 26	42 -- 48	-13.8545 kcal/mol	1.95631 kcal/mol	3.26026 kcal/mol	16 27@LB@ \| \|@LB@5'-GAA...AAAAG UUGCC...UGC-3'@LB@ UGCGUGAAGU@LB@ \|:\|\|\|\|\|\|\|\|@LB@ AUGCACUUCA@LB@3'-AUU...GGCUA UUUUC...AUG-5'@LB@ \| \|@LB@ 52 41@LB@@LB@@LB@Energy -8.65 kcal/mol@LB@Hybridization Energy -13.8545 kcal/mol@LB@Unfolding Energy - mRNA 1.95631 kcal/mol@LB@Unfolding Energy - sRNA 3.26026 kcal/mol@LB@@LB@Position - mRNA 17 -- 26@LB@Position - sRNA 42 -- 51@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 42 -- 48@LB@
129	0.004413	0.1199	b0062	araA	-8.60	0.109835	267 -- 273	1 -- 7	L-arabinose isomerase	_____________266_____274\n_____________\|_______\|\n5'-CGC...CGGAA_______GUCAG...ACG-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	267 -- 273	1 -- 7	-12.3746 kcal/mol	1.75625 kcal/mol	2.03949 kcal/mol	266 274@LB@ \| \|@LB@5'-CGC...CGGAA GUCAG...ACG-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.3746 kcal/mol@LB@Unfolding Energy - mRNA 1.75625 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 267 -- 273@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
185	0.008247	0.1556	b4195	ulaC	-8.57	0.111851	181 -- 191	40 -- 50	L-ascorbate-specific enzyme IIA component of PTS	_____________180_________192\n_____________\|___________\|\n5'-GCG...GCAGG___________GGACG...UGG-3'\n______________AUGUGAAGUAA\n______________\|:\|\|\|\|\|\|\|\|\|\n______________UGCACUUCAUU\n3'-AUU...GCUAA___________UUCCA...AUG-5'\n_____________\|___________\|\n_____________51__________39\n	185 -- 191	40 -- 46	-13.163 kcal/mol	1.2893 kcal/mol	3.32158 kcal/mol	180 192@LB@ \| \|@LB@5'-GCG...GCAGG GGACG...UGG-3'@LB@ AUGUGAAGUAA@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ UGCACUUCAUU@LB@3'-AUU...GCUAA UUCCA...AUG-5'@LB@ \| \|@LB@ 51 39@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -13.163 kcal/mol@LB@Unfolding Energy - mRNA 1.2893 kcal/mol@LB@Unfolding Energy - sRNA 3.32158 kcal/mol@LB@@LB@Position - mRNA 181 -- 191@LB@Position - sRNA 40 -- 50@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 40 -- 46@LB@
155	0.00623	0.1406	b4178	nsrR	-8.53	0.114937	220 -- 228	48 -- 56	nitric oxide-sensitive repressor for NO regulon	_____________219_______229\n_____________\|_________\|\n5'-GGU...UUUCA_________GAUUA...ACG-3'\n______________CUGAUUACG\n______________\|:\|\|\|\|\|\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	222 -- 228	48 -- 54	-11.8869 kcal/mol	1.78283 kcal/mol	1.55919 kcal/mol	219 229@LB@ \| \|@LB@5'-GGU...UUUCA GAUUA...ACG-3'@LB@ CUGAUUACG@LB@ \|:\|\|\|\|\|\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -11.8869 kcal/mol@LB@Unfolding Energy - mRNA 1.78283 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 220 -- 228@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 48 -- 54@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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