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
161	0.006501	0.1413	b2682	ygaZ	-8.47	0.118892	208 -- 214	1 -- 7	putative L-valine exporter norvaline resistance protein		_____________207_____215\n_____________\|_______\|\n5'-UGG...GGAAA_______UCCAC...CCU-3'\n______________GCCCUAC\n______________:\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	208 -- 214	1 -- 7	-11.2451 kcal/mol	0.761293 kcal/mol	2.03949 kcal/mol	207 215@LB@ \| \|@LB@5'-UGG...GGAAA UCCAC...CCU-3'@LB@ GCCCUAC@LB@ :\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -11.2451 kcal/mol@LB@Unfolding Energy - mRNA 0.761293 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 208 -- 214@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 1 -- 7@LB@
162	0.006534	0.1413	b3771	ilvD	-6.87	0.280008	44 -- 51	49 -- 56	dihydroxyacid dehydratase		_____________43_______52\n_____________\|________\|\n5'-GCG...GUGGC________CAAAC...GUA-3'\n______________CCGGUUAC\n______________\|\|\|:\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	45 -- 51	49 -- 55	-9.72973 kcal/mol	2.55538 kcal/mol	0.317884 kcal/mol	43 52@LB@ \| \|@LB@5'-GCG...GUGGC CAAAC...GUA-3'@LB@ CCGGUUAC@LB@ \|\|\|:\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -6.87 kcal/mol@LB@Hybridization Energy -9.72973 kcal/mol@LB@Unfolding Energy - mRNA 2.55538 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 44 -- 51@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 49 -- 55@LB@
163	0.006545	0.1413	b0532	sfmD	-7.71	0.181786	104 -- 132	48 -- 76	putative outer membrane export usher protein	b3144 b4317 b0940	_____________103____________________________133\n_____________\|______________________________\|\n5'-UCA...GGAAA______________A___UUAA________GUUCA...GCU-3'\n______________GCUGAAAU_UUCAG_CCG____UGAUUAUG\n______________\|\|\|:\|\|\|\|_\|\|\|\|\|_\|\|:____:\|\|\|\|\|:\|\n______________CGAUUUUA_AAGUC_GGU____GCUAAUGC\n3'-AUU...CCCGC________U_________UUAG________ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________77_____________________________47\n	126 -- 132	48 -- 54	-23.9612 kcal/mol	8.59534 kcal/mol	7.67378 kcal/mol	103 133@LB@ \| \|@LB@5'-UCA...GGAAA A UUAA GUUCA...GCU-3'@LB@ GCUGAAAU UUCAG CCG UGAUUAUG@LB@ \|\|\|:\|\|\|\| \|\|\|\|\| \|\|: :\|\|\|\|\|:\|@LB@ CGAUUUUA AAGUC GGU GCUAAUGC@LB@3'-AUU...CCCGC U UUAG ACUUC...AUG-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -23.9612 kcal/mol@LB@Unfolding Energy - mRNA 8.59534 kcal/mol@LB@Unfolding Energy - sRNA 7.67378 kcal/mol@LB@@LB@Position - mRNA 104 -- 132@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 48 -- 54@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@
165	0.006672	0.1423	b1651	gloA	-7.94	0.160716	101 -- 108	49 -- 56	glyoxalase I Ni-dependent		_____________100______109\n_____________\|________\|\n5'-UGG...CUAUA________CCGAC...AAA-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	102 -- 108	49 -- 55	-10.6899 kcal/mol	2.44421 kcal/mol	0.317884 kcal/mol	100 109@LB@ \| \|@LB@5'-UGG...CUAUA CCGAC...AAA-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -7.94 kcal/mol@LB@Hybridization Energy -10.6899 kcal/mol@LB@Unfolding Energy - mRNA 2.44421 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 101 -- 108@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 49 -- 55@LB@
166	0.006804	0.1439	b0475	hemH	-7.56	0.197603	220 -- 228	1 -- 9	ferrochelatase		_____________219_______229\n_____________\|_________\|\n5'-CGG...AACCG_________UGGCA...GCG-3'\n______________GUAUCCUGC\n______________\|\|\|:\|\|\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	222 -- 228	1 -- 7	-12.5413 kcal/mol	2.87943 kcal/mol	2.12872 kcal/mol	219 229@LB@ \| \|@LB@5'-CGG...AACCG UGGCA...GCG-3'@LB@ GUAUCCUGC@LB@ \|\|\|:\|\|\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.56 kcal/mol@LB@Hybridization Energy -12.5413 kcal/mol@LB@Unfolding Energy - mRNA 2.87943 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 220 -- 228@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 1 -- 7@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@
168	0.006917	0.1448	b3070	yqjH	-8.25	0.134865	172 -- 181	49 -- 58	putative siderophore interacting protein		_____________171________182\n_____________\|__________\|\n5'-ACU...GAUAU__________CAUCA...AGC-3'\n______________AUCUGAUUAC\n______________\|\|\|:\|\|\|\|\|\|\n______________UAGGCUAAUG\n3'-AUU...CGGUU__________CACUU...AUG-5'\n_____________\|__________\|\n_____________59_________48\n	175 -- 181	49 -- 55	-10.8722 kcal/mol	2.31397 kcal/mol	0.318367 kcal/mol	171 182@LB@ \| \|@LB@5'-ACU...GAUAU CAUCA...AGC-3'@LB@ AUCUGAUUAC@LB@ \|\|\|:\|\|\|\|\|\|@LB@ UAGGCUAAUG@LB@3'-AUU...CGGUU CACUU...AUG-5'@LB@ \| \|@LB@ 59 48@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -10.8722 kcal/mol@LB@Unfolding Energy - mRNA 2.31397 kcal/mol@LB@Unfolding Energy - sRNA 0.318367 kcal/mol@LB@@LB@Position - mRNA 172 -- 181@LB@Position - sRNA 49 -- 58@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 49 -- 55@LB@
169	0.006985	0.1454	b0384	psiF	-5.27	0.543574	221 -- 228	1 -- 8	PsiF family protein		_____________220______229\n_____________\|________\|\n5'-CCC...CUGGU________UUUUC...UGA-3'\n______________UACCUUGC\n______________\|\|\|\|:\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	222 -- 228	1 -- 7	-9.62499 kcal/mol	2.26355 kcal/mol	2.11603 kcal/mol	220 229@LB@ \| \|@LB@5'-CCC...CUGGU UUUUC...UGA-3'@LB@ UACCUUGC@LB@ \|\|\|\|:\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -5.27 kcal/mol@LB@Hybridization Energy -9.62499 kcal/mol@LB@Unfolding Energy - mRNA 2.26355 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 221 -- 228@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 1 -- 7@LB@
170	0.007042	0.1457	b3110	yhaO	-10.02	0.044877	174 -- 180	1 -- 7	putative transporter		_____________173_____181\n_____________\|_______\|\n5'-AAU...AAUAA_______AAAAU...UCG-3'\n______________GCCCUAC\n______________:\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	174 -- 180	1 -- 7	-12.6531 kcal/mol	0.621925 kcal/mol	2.03949 kcal/mol	173 181@LB@ \| \|@LB@5'-AAU...AAUAA AAAAU...UCG-3'@LB@ GCCCUAC@LB@ :\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -12.6531 kcal/mol@LB@Unfolding Energy - mRNA 0.621925 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 174 -- 180@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 1 -- 7@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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