Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
38	0.00253	0.2088	b3789	rffH	-8.84	0.205897	98 -- 106	51 -- 59	glucose-1-phosphate thymidylyltransferase	_____________97________107\n_____________\|_________\|\n5'-GGC...ACGGU_________UCUGG...UGA-3'\n______________UCAGUGGUA\n______________\|\|\|\|\|\|\|:\|\n______________AGUCACCGU\n3'-UUU...CUUUU_________UACGU...UUG-5'\n_____________\|_________\|\n_____________60________50\n	100 -- 106	51 -- 57	-13.9039 kcal/mol	2.34576 kcal/mol	2.71896 kcal/mol	97 107@LB@ \| \|@LB@5'-GGC...ACGGU UCUGG...UGA-3'@LB@ UCAGUGGUA@LB@ \|\|\|\|\|\|\|:\|@LB@ AGUCACCGU@LB@3'-UUU...CUUUU UACGU...UUG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -13.9039 kcal/mol@LB@Unfolding Energy - mRNA 2.34576 kcal/mol@LB@Unfolding Energy - sRNA 2.71896 kcal/mol@LB@@LB@Position - mRNA 98 -- 106@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 51 -- 57@LB@
64	0.005005	0.2614	b3795	yifK	-6.27	0.531551	193 -- 206	51 -- 64	putative APC family amino acid transporter	_____________192____________207\n_____________\|______________\|\n5'-CAA...AACAC_______UA_____GAUAA...GGG-3'\n______________GAGGAUU__UGGCA\n______________\|\|::\|\|:__\|\|\|\|\|\n______________CUUUUAG__ACCGU\n3'-UUU...ACAAC_______UC_____UACGU...UUG-5'\n_____________\|______________\|\n_____________65_____________50\n	193 -- 199	58 -- 64	-12.618 kcal/mol	3.46106 kcal/mol	2.8882 kcal/mol	192 207@LB@ \| \|@LB@5'-CAA...AACAC UA GAUAA...GGG-3'@LB@ GAGGAUU UGGCA@LB@ \|\|::\|\|: \|\|\|\|\|@LB@ CUUUUAG ACCGU@LB@3'-UUU...ACAAC UC UACGU...UUG-5'@LB@ \| \|@LB@ 65 50@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -12.618 kcal/mol@LB@Unfolding Energy - mRNA 3.46106 kcal/mol@LB@Unfolding Energy - sRNA 2.8882 kcal/mol@LB@@LB@Position - mRNA 193 -- 206@LB@Position - sRNA 51 -- 64@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 58 -- 64@LB@
191	0.02382	0.4194	b4567	yjjZ	-11.31	0.063816	288 -- 298	51 -- 61	uncharacterized protein	_____________287_________299\n_____________\|___________\|\n5'-CGG...CGUCA___________GA-3'\n______________GAUCAGUGGCG\n______________:\|\|\|\|\|\|\|\|\|:\n______________UUAGUCACCGU\n3'-UUU...ACCUU___________UACGU...UUG-5'\n_____________\|___________\|\n_____________62__________50\n	292 -- 298	51 -- 57	-17.6489 kcal/mol	3.61415 kcal/mol	2.72961 kcal/mol	287 299@LB@ \| \|@LB@5'-CGG...CGUCA GA-3'@LB@ GAUCAGUGGCG@LB@ :\|\|\|\|\|\|\|\|\|:@LB@ UUAGUCACCGU@LB@3'-UUU...ACCUU UACGU...UUG-5'@LB@ \| \|@LB@ 62 50@LB@@LB@@LB@Energy -11.31 kcal/mol@LB@Hybridization Energy -17.6489 kcal/mol@LB@Unfolding Energy - mRNA 3.61415 kcal/mol@LB@Unfolding Energy - sRNA 2.72961 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 51 -- 61@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 51 -- 57@LB@
108	0.01004	0.3126	b2422	cysA	-10.23	0.108830	144 -- 158	52 -- 72	sulfate/thiosulfate transporter subunit	_____________143___________________159\n_____________\|_____________________\|\n5'-GGU...AAAAA_____________________GCCUG...UGC-3'\n______________GUAUGUUG______CAGUGGC\n______________:\|\|\|\|\|\|\|______\|\|\|\|\|\|\|\n______________UAUACAAC______GUCACCG\n3'-UUU...AAAAA________CUUUUA_______UUACG...UUG-5'\n_____________\|_____________________\|\n_____________73____________________51\n	152 -- 158	52 -- 58	-18.4697 kcal/mol	5.08596 kcal/mol	3.1495 kcal/mol	143 159@LB@ \| \|@LB@5'-GGU...AAAAA GCCUG...UGC-3'@LB@ GUAUGUUG CAGUGGC@LB@ :\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UAUACAAC GUCACCG@LB@3'-UUU...AAAAA CUUUUA UUACG...UUG-5'@LB@ \| \|@LB@ 73 51@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -18.4697 kcal/mol@LB@Unfolding Energy - mRNA 5.08596 kcal/mol@LB@Unfolding Energy - sRNA 3.1495 kcal/mol@LB@@LB@Position - mRNA 144 -- 158@LB@Position - sRNA 52 -- 72@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 52 -- 58@LB@
172	0.02065	0.4033	b1015	putP	-10.70	0.086688	188 -- 205	52 -- 67	proline:sodium symporter	_____________187________________206\n_____________\|__________________\|\n5'-AGA...AUUUU_______CU____A____UAUUA...ACG-3'\n______________UUGGAGA__UUAG_UGGC\n______________\|\|\|\|\|:\|__\|:\|\|_\|\|\|\|\n______________AACCUUU__AGUC_ACCG\n3'-UUU...UAUAC_______U__________UUACG...UUG-5'\n_____________\|__________________\|\n_____________68_________________51\n	188 -- 194	61 -- 67	-15.9795 kcal/mol	2.37428 kcal/mol	2.90583 kcal/mol	187 206@LB@ \| \|@LB@5'-AGA...AUUUU CU A UAUUA...ACG-3'@LB@ UUGGAGA UUAG UGGC@LB@ \|\|\|\|\|:\| \|:\|\| \|\|\|\|@LB@ AACCUUU AGUC ACCG@LB@3'-UUU...UAUAC U UUACG...UUG-5'@LB@ \| \|@LB@ 68 51@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -15.9795 kcal/mol@LB@Unfolding Energy - mRNA 2.37428 kcal/mol@LB@Unfolding Energy - sRNA 2.90583 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 52 -- 67@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 61 -- 67@LB@
139	0.0159	0.3828	b2108	yehA	-9.84	0.131393	50 -- 60	55 -- 65	putative fimbrial-like adhesin protein	_____________49__________61\n_____________\|___________\|\n5'-GUU...GGCCA___________UAUUU...UUG-3'\n______________GGGAAGUCAGU\n______________\|\|:\|\|:\|\|\|\|\|\n______________CCUUUUAGUCA\n3'-UUU...UACAA___________CCGUU...UUG-5'\n_____________\|___________\|\n_____________66__________54\n	54 -- 60	55 -- 61	-13.8721 kcal/mol	3.08221 kcal/mol	0.952476 kcal/mol	49 61@LB@ \| \|@LB@5'-GUU...GGCCA UAUUU...UUG-3'@LB@ GGGAAGUCAGU@LB@ \|\|:\|\|:\|\|\|\|\|@LB@ CCUUUUAGUCA@LB@3'-UUU...UACAA CCGUU...UUG-5'@LB@ \| \|@LB@ 66 54@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -13.8721 kcal/mol@LB@Unfolding Energy - mRNA 3.08221 kcal/mol@LB@Unfolding Energy - sRNA 0.952476 kcal/mol@LB@@LB@Position - mRNA 50 -- 60@LB@Position - sRNA 55 -- 65@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 55 -- 61@LB@
196	0.02524	0.4256	b1805	fadD	-8.19	0.269381	280 -- 298	55 -- 72	acyl-CoA synthetase (long-chain-fatty-acid--CoA ligase)	_____________279_________________299\n_____________\|___________________\|\n5'-UUG...GGUAG_______U___C_______CG-3'\n______________AUAUGUU_GAG_AGUCGGU\n______________\|\|\|\|\|\|\|_\|\|:_\|:\|\|:\|\|\n______________UAUACAA_CUU_UUAGUCA\n3'-UUU...AAAAA_______C___________CCGUU...UUG-5'\n_____________\|___________________\|\n_____________73__________________54\n	292 -- 298	55 -- 61	-14.048 kcal/mol	3.20699 kcal/mol	2.64594 kcal/mol	279 299@LB@ \| \|@LB@5'-UUG...GGUAG U C CG-3'@LB@ AUAUGUU GAG AGUCGGU@LB@ \|\|\|\|\|\|\| \|\|: \|:\|\|:\|\|@LB@ UAUACAA CUU UUAGUCA@LB@3'-UUU...AAAAA C CCGUU...UUG-5'@LB@ \| \|@LB@ 73 54@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -14.048 kcal/mol@LB@Unfolding Energy - mRNA 3.20699 kcal/mol@LB@Unfolding Energy - sRNA 2.64594 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 55 -- 72@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 55 -- 61@LB@
182	0.02271	0.4143	b1686	menI	-7.81	0.313804	214 -- 222	57 -- 65	1 4-dihydroxy-2-naphthoyl-CoA hydrolase	_____________213_______223\n_____________\|_________\|\n5'-GGC...GAAAC_________CCCUG...AUG-3'\n______________GGAAAAUCA\n______________\|\|\|\|\|\|\|\|\|\n______________CCUUUUAGU\n3'-UUU...UACAA_________CACCG...UUG-5'\n_____________\|_________\|\n_____________66________56\n	216 -- 222	57 -- 63	-11.126 kcal/mol	2.47866 kcal/mol	0.839876 kcal/mol	213 223@LB@ \| \|@LB@5'-GGC...GAAAC CCCUG...AUG-3'@LB@ GGAAAAUCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCUUUUAGU@LB@3'-UUU...UACAA CACCG...UUG-5'@LB@ \| \|@LB@ 66 56@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -11.126 kcal/mol@LB@Unfolding Energy - mRNA 2.47866 kcal/mol@LB@Unfolding Energy - sRNA 0.839876 kcal/mol@LB@@LB@Position - mRNA 214 -- 222@LB@Position - sRNA 57 -- 65@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 57 -- 63@LB@
126	0.01341	0.3578	b3572	avtA	-7.69	0.327921	259 -- 267	58 -- 66	valine-pyruvate aminotransferase; transaminase C; alanine-valine transaminase	_____________258_______268\n_____________\|_________\|\n5'-UCG...GUUGA_________UGAAC...UUA-3'\n______________UGGAAGAUC\n______________\|\|\|\|\|:\|\|\|\n______________ACCUUUUAG\n3'-UUU...AUACA_________UCACC...UUG-5'\n_____________\|_________\|\n_____________67________57\n	261 -- 267	58 -- 64	-10.9576 kcal/mol	2.42155 kcal/mol	0.843879 kcal/mol	258 268@LB@ \| \|@LB@5'-UCG...GUUGA UGAAC...UUA-3'@LB@ UGGAAGAUC@LB@ \|\|\|\|\|:\|\|\|@LB@ ACCUUUUAG@LB@3'-UUU...AUACA UCACC...UUG-5'@LB@ \| \|@LB@ 67 57@LB@@LB@@LB@Energy -7.69 kcal/mol@LB@Hybridization Energy -10.9576 kcal/mol@LB@Unfolding Energy - mRNA 2.42155 kcal/mol@LB@Unfolding Energy - sRNA 0.843879 kcal/mol@LB@@LB@Position - mRNA 259 -- 267@LB@Position - sRNA 58 -- 66@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 58 -- 64@LB@
194	0.0246	0.4256	b0211	mltD	-5.59	0.639593	30 -- 36	59 -- 65	putative membrane-bound lytic murein transglycosylase D	_____________29______37\n_____________\|_______\|\n5'-GAG...AGAAC_______AUUGA...GUC-3'\n______________GGAAGAU\n______________\|\|\|\|:\|\|\n______________CCUUUUA\n3'-UUU...UACAA_______GUCAC...UUG-5'\n_____________\|_______\|\n_____________66______58\n	30 -- 36	59 -- 65	-7.35578 kcal/mol	0.945124 kcal/mol	0.81955 kcal/mol	29 37@LB@ \| \|@LB@5'-GAG...AGAAC AUUGA...GUC-3'@LB@ GGAAGAU@LB@ \|\|\|\|:\|\|@LB@ CCUUUUA@LB@3'-UUU...UACAA GUCAC...UUG-5'@LB@ \| \|@LB@ 66 58@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -7.35578 kcal/mol@LB@Unfolding Energy - mRNA 0.945124 kcal/mol@LB@Unfolding Energy - sRNA 0.81955 kcal/mol@LB@@LB@Position - mRNA 30 -- 36@LB@Position - sRNA 59 -- 65@LB@Position Seed - mRNA 30 -- 36@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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