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
181	0.007802	0.1516	b1797	yeaR	-7.07	0.254063	142 -- 149	2 -- 9	DUF1971 family protein nitrate-inducible	_____________141______150\n_____________\|________\|\n5'-UGC...CAGGC________AAACG...AAG-3'\n______________GUACCCUG\n______________\|\|\|\|\|\|\|:\n______________CAUGGGAU\n3'-AUU...GGAGA________G-5'\n_____________\|________\|\n_____________10_______1\n	143 -- 149	2 -- 8	-12.2602 kcal/mol	3.09143 kcal/mol	2.12684 kcal/mol	141 150@LB@ \| \|@LB@5'-UGC...CAGGC AAACG...AAG-3'@LB@ GUACCCUG@LB@ \|\|\|\|\|\|\|:@LB@ CAUGGGAU@LB@3'-AUU...GGAGA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.07 kcal/mol@LB@Hybridization Energy -12.2602 kcal/mol@LB@Unfolding Energy - mRNA 3.09143 kcal/mol@LB@Unfolding Energy - sRNA 2.12684 kcal/mol@LB@@LB@Position - mRNA 142 -- 149@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 2 -- 8@LB@
182	0.007896	0.1519	b0686	ybfF	-7.34	0.221050	164 -- 170	2 -- 8	acyl-CoA esterase	_____________163_____171\n_____________\|_______\|\n5'-CUU...CAUAA_______ACCCG...GCG-3'\n______________UACCCUA\n______________\|\|\|\|\|\|\|\n______________AUGGGAU\n3'-AUU...GAGAC_______G-5'\n_____________\|_______\|\n_____________9_______1\n	164 -- 170	2 -- 8	-9.7212 kcal/mol	0.292492 kcal/mol	2.11083 kcal/mol	163 171@LB@ \| \|@LB@5'-CUU...CAUAA ACCCG...GCG-3'@LB@ UACCCUA@LB@ \|\|\|\|\|\|\|@LB@ AUGGGAU@LB@3'-AUU...GAGAC G-5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -7.34 kcal/mol@LB@Hybridization Energy -9.7212 kcal/mol@LB@Unfolding Energy - mRNA 0.292492 kcal/mol@LB@Unfolding Energy - sRNA 2.11083 kcal/mol@LB@@LB@Position - mRNA 164 -- 170@LB@Position - sRNA 2 -- 8@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 2 -- 8@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@
184	0.00812	0.1553	b4371	rsmC	-7.50	0.203534	191 -- 216	4 -- 25	16S rRNA m(2)G1207 methyltransferase SAM-dependent	_____________190________________________217\n_____________\|__________________________\|\n5'-AUC...AUUGA________CC__G____CAUU_____CGGCA...UGC-3'\n______________GGAGCAUU__AU_UCUG____UACCC\n______________:\|\|:\|\|\|:__\|:_\|\|\|\|____\|\|\|\|\|\n______________UCUUGUAG__UG_AGAC____AUGGG\n3'-AUU...UUCUA________AA__G_____________AUG-5'\n_____________\|__________________________\|\n_____________26_________________________3\n	192 -- 198	18 -- 24	-20.5319 kcal/mol	5.03265 kcal/mol	8.0209 kcal/mol	190 217@LB@ \| \|@LB@5'-AUC...AUUGA CC G CAUU CGGCA...UGC-3'@LB@ GGAGCAUU AU UCUG UACCC@LB@ :\|\|:\|\|\|: \|: \|\|\|\| \|\|\|\|\|@LB@ UCUUGUAG UG AGAC AUGGG@LB@3'-AUU...UUCUA AA G AUG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -20.5319 kcal/mol@LB@Unfolding Energy - mRNA 5.03265 kcal/mol@LB@Unfolding Energy - sRNA 8.0209 kcal/mol@LB@@LB@Position - mRNA 191 -- 216@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 18 -- 24@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@
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@
187	0.008276	0.1556	b0827	moeA	-6.51	0.330510	82 -- 91	23 -- 32	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein	_____________81_________92\n_____________\|__________\|\n5'-AUU...AUAUA__________UAUGG...UAC-3'\n______________GAAAGAUGGA\n______________\|\|\|\|\|\|\|:\|\|\n______________CUUUCUAUCU\n3'-AUU...CCAGA__________UGUAG...AUG-5'\n_____________\|__________\|\n_____________33_________22\n	85 -- 91	23 -- 29	-12.1772 kcal/mol	2.37895 kcal/mol	3.23951 kcal/mol	81 92@LB@ \| \|@LB@5'-AUU...AUAUA UAUGG...UAC-3'@LB@ GAAAGAUGGA@LB@ \|\|\|\|\|\|\|:\|\|@LB@ CUUUCUAUCU@LB@3'-AUU...CCAGA UGUAG...AUG-5'@LB@ \| \|@LB@ 33 22@LB@@LB@@LB@Energy -6.51 kcal/mol@LB@Hybridization Energy -12.1772 kcal/mol@LB@Unfolding Energy - mRNA 2.37895 kcal/mol@LB@Unfolding Energy - sRNA 3.23951 kcal/mol@LB@@LB@Position - mRNA 82 -- 91@LB@Position - sRNA 23 -- 32@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 23 -- 29@LB@
188	0.008316	0.1556	b3406	greB	-8.11	0.146040	42 -- 55	52 -- 65	transcript cleavage factor	_____________41_____________56\n_____________\|______________\|\n5'-AUU...GUCAC______________AUGAA...UGA-3'\n______________CAGCUAAAUCUGGU\n______________\|\|\|\|:\|\|\|\|\|:\|:\|\n______________GUCGGUUUAGGCUA\n3'-AUU...UAUAA______________AUGCA...AUG-5'\n_____________\|______________\|\n_____________66_____________51\n	49 -- 55	52 -- 58	-18.5321 kcal/mol	4.27254 kcal/mol	6.17277 kcal/mol	41 56@LB@ \| \|@LB@5'-AUU...GUCAC AUGAA...UGA-3'@LB@ CAGCUAAAUCUGGU@LB@ \|\|\|\|:\|\|\|\|\|:\|:\|@LB@ GUCGGUUUAGGCUA@LB@3'-AUU...UAUAA AUGCA...AUG-5'@LB@ \| \|@LB@ 66 51@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -18.5321 kcal/mol@LB@Unfolding Energy - mRNA 4.27254 kcal/mol@LB@Unfolding Energy - sRNA 6.17277 kcal/mol@LB@@LB@Position - mRNA 42 -- 55@LB@Position - sRNA 52 -- 65@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 52 -- 58@LB@
189	0.008373	0.1558	b1559	quuQ	-11.90	0.011421	197 -- 219	1 -- 24	Qin prophage; putative antitermination protein Q	_____________196______________________220\n_____________\|________________________\|\n5'-UCU...AGAAC______GA______GAA_______CAAAA...AUG-3'\n______________GAGCAU___ACCUU___GCCUUAC\n______________\|\|:\|\|\|___\|\|\|\|:___:\|\|:\|\|\|\n______________CUUGUA___UGGAG___UGGGAUG\n3'-AUU...UCUAU______GAA_____ACA_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	213 -- 219	1 -- 7	-21.9861 kcal/mol	2.0909 kcal/mol	8.02158 kcal/mol	196 220@LB@ \| \|@LB@5'-UCU...AGAAC GA GAA CAAAA...AUG-3'@LB@ GAGCAU ACCUU GCCUUAC@LB@ \|\|:\|\|\| \|\|\|\|: :\|\|:\|\|\|@LB@ CUUGUA UGGAG UGGGAUG@LB@3'-AUU...UCUAU GAA ACA -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -21.9861 kcal/mol@LB@Unfolding Energy - mRNA 2.0909 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 197 -- 219@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 1 -- 7@LB@
190	0.008456	0.1558	b0036	caiD	-8.40	0.123663	110 -- 117	1 -- 8	carnitinyl-CoA dehydratase	_____________109______118\n_____________\|________\|\n5'-UGG...GGAAC________CAGCU...AAA-3'\n______________UACCCUGC\n______________\|\|\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	111 -- 117	1 -- 7	-12.4513 kcal/mol	1.95818 kcal/mol	2.11603 kcal/mol	109 118@LB@ \| \|@LB@5'-UGG...GGAAC CAGCU...AAA-3'@LB@ UACCCUGC@LB@ \|\|\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -12.4513 kcal/mol@LB@Unfolding Energy - mRNA 1.95818 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 110 -- 117@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 111 -- 117@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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