Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
79	0.005218	0.2128	b1264	trpE	-7.84	0.066605	225 -- 250	34 -- 59	component I of anthranilate synthase	_____________224__________________________251\n_____________\|____________________________\|\n5'-UGU...CUCUC_________AACCU______________UCGCG...CGG-3'\n______________GAAC_UGCU_____GCGA_AGGCGCUUA\n______________:\|\|\|_\|\|\|\|_____\|\|:\|_\|:\|\|:\|\|\|\|\n______________UUUG_ACGA_____CGUU_UUCGUGAAU\n3'-UUU...CCUAC____A____AUU______C_________UUUUU...CAA-5'\n_____________\|____________________________\|\n_____________60___________________________33\n	244 -- 250	34 -- 40	-20.2106 kcal/mol	6.10702 kcal/mol	6.26371 kcal/mol	224 251@LB@ \| \|@LB@5'-UGU...CUCUC AACCU UCGCG...CGG-3'@LB@ GAAC UGCU GCGA AGGCGCUUA@LB@ :\|\|\| \|\|\|\| \|\|:\| \|:\|\|:\|\|\|\|@LB@ UUUG ACGA CGUU UUCGUGAAU@LB@3'-UUU...CCUAC A AUU C UUUUU...CAA-5'@LB@ \| \|@LB@ 60 33@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -20.2106 kcal/mol@LB@Unfolding Energy - mRNA 6.10702 kcal/mol@LB@Unfolding Energy - sRNA 6.26371 kcal/mol@LB@@LB@Position - mRNA 225 -- 250@LB@Position - sRNA 34 -- 59@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 34 -- 40@LB@
182	0.02157	0.3768	b0887	cydD	-7.84	0.066788	30 -- 38	33 -- 41	glutathione/cysteine ABC transporter export permease/ATPase	_____________29________39\n_____________\|_________\|\n5'-AUU...AUGGC_________UGCGG...UGA-3'\n______________AGCACUUGA\n______________\|\|\|\|\|\|\|:\|\n______________UCGUGAAUU\n3'-UUU...GUUCU_________UUUUA...CAA-5'\n_____________\|_________\|\n_____________42________32\n	32 -- 38	33 -- 39	-10.6359 kcal/mol	1.18174 kcal/mol	1.6188 kcal/mol	29 39@LB@ \| \|@LB@5'-AUU...AUGGC UGCGG...UGA-3'@LB@ AGCACUUGA@LB@ \|\|\|\|\|\|\|:\|@LB@ UCGUGAAUU@LB@3'-UUU...GUUCU UUUUA...CAA-5'@LB@ \| \|@LB@ 42 32@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -10.6359 kcal/mol@LB@Unfolding Energy - mRNA 1.18174 kcal/mol@LB@Unfolding Energy - sRNA 1.6188 kcal/mol@LB@@LB@Position - mRNA 30 -- 38@LB@Position - sRNA 33 -- 41@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 33 -- 39@LB@
146	0.01469	0.3231	b0026	ileS	-7.82	0.067581	147 -- 206	2 -- 59	isoleucyl-tRNA synthetase	_____________146_____________________________________________________________207\n_____________\|_______________________________________________________________\|\n5'-AUG...UAACA____CG________CU_UUAU___AUCAAACC_____A__GA______A___________A__GACUA...CUG-3'\n______________AAAC__GCUUAAGC__G____GUA________GAAAU_CG____ACCG__GAAUCUGAUG_GU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|__\|____\|:\|________:\|\|\|\|_\|\|____\|\|\|:__:\|\|\|\|\|\|\|\|\|_\|\|\n______________UUUG__CGAAUUCG__C____CGU________UUUUA_GC____UGGU__UUUAGACUAC_CA\n3'-UUU...CCUAC____AA________UU_UU_____GAAUU________A__AAUG____CC__________A__A-5'\n_____________\|_______________________________________________________________\|\n_____________60______________________________________________________________1\n	197 -- 203	5 -- 11	-33.6314 kcal/mol	11.9684 kcal/mol	13.8468 kcal/mol	146 207@LB@ \| \|@LB@5'-AUG...UAACA CG CU UUAU AUCAAACC A GA A A GACUA...CUG-3'@LB@ AAAC GCUUAAGC G GUA GAAAU CG ACCG GAAUCUGAUG GU@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \| \|:\| :\|\|\|\| \|\| \|\|\|: :\|\|\|\|\|\|\|\|\| \|\|@LB@ UUUG CGAAUUCG C CGU UUUUA GC UGGU UUUAGACUAC CA@LB@3'-UUU...CCUAC AA UU UU GAAUU A AAUG CC A A-5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -7.82 kcal/mol@LB@Hybridization Energy -33.6314 kcal/mol@LB@Unfolding Energy - mRNA 11.9684 kcal/mol@LB@Unfolding Energy - sRNA 13.8468 kcal/mol@LB@@LB@Position - mRNA 147 -- 206@LB@Position - sRNA 2 -- 59@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 5 -- 11@LB@
72	0.003773	0.1688	b1860	ruvB	-7.81	0.067658	103 -- 111	38 -- 46	ATP-dependent DNA helicase component of RuvABC resolvasome	_____________102_______112\n_____________\|_________\|\n5'-ACG...AACCA_________AGCCG...GUC-3'\n______________CAAGAAGCA\n______________\|\|\|\|\|\|\|\|\|\n______________GUUCUUCGU\n3'-UUU...AAUUC_________GAAUU...CAA-5'\n_____________\|_________\|\n_____________47________37\n	105 -- 111	38 -- 44	-11.4188 kcal/mol	0.978333 kcal/mol	2.62609 kcal/mol	102 112@LB@ \| \|@LB@5'-ACG...AACCA AGCCG...GUC-3'@LB@ CAAGAAGCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GUUCUUCGU@LB@3'-UUU...AAUUC GAAUU...CAA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -11.4188 kcal/mol@LB@Unfolding Energy - mRNA 0.978333 kcal/mol@LB@Unfolding Energy - sRNA 2.62609 kcal/mol@LB@@LB@Position - mRNA 103 -- 111@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 38 -- 44@LB@
181	0.0215	0.3768	b3843	ubiD	-7.81	0.067872	2 -- 28	14 -- 40	3-octaprenyl-4-hydroxybenzoate decarboxylase	_____________1____________________________29\n_____________\|____________________________\|\n__________5'-C_______CAGUACA___AA_________UUGCA...UGG-3'\n______________GCGCUUG________GU__AUACCAGGA\n______________\|\|:\|\|\|:________\|\|__\|:\|\|\|\|\|\|\|\n______________CGUGAAU________CA__UGUGGUCCU\n3'-UUU...UUCUU_______UUUUUAAG__A__________UUAGA...CAA-5'\n_____________\|____________________________\|\n_____________41___________________________13\n	22 -- 28	14 -- 20	-21.9915 kcal/mol	4.97788 kcal/mol	9.20436 kcal/mol	1 29@LB@ \| \|@LB@ 5'-C CAGUACA AA UUGCA...UGG-3'@LB@ GCGCUUG GU AUACCAGGA@LB@ \|\|:\|\|\|: \|\| \|:\|\|\|\|\|\|\|@LB@ CGUGAAU CA UGUGGUCCU@LB@3'-UUU...UUCUU UUUUUAAG A UUAGA...CAA-5'@LB@ \| \|@LB@ 41 13@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -21.9915 kcal/mol@LB@Unfolding Energy - mRNA 4.97788 kcal/mol@LB@Unfolding Energy - sRNA 9.20436 kcal/mol@LB@@LB@Position - mRNA 2 -- 28@LB@Position - sRNA 14 -- 40@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 14 -- 20@LB@
195	0.02349	0.3864	b3982	nusG	-7.66	0.074558	21 -- 55	24 -- 55	transcription termination factor	_____________20__________________________________56\n_____________\|___________________________________\|\n5'-GAC...UACCG______UU__CCGU_______GUACC_____C___AAGGU...ACA-3'\n______________UUGCUU__GC____GAAGCGC_____GAAGU_CGU\n______________\|\|\|\|\|\|__\|\|____\|\|\|\|\|:\|_____:\|\|:\|_\|\|\|\n______________AACGAA__CG____CUUCGUG_____UUUUA_GCA\n3'-UUU...CUUUG______UU__UU_________AAUU______A___AUGUG...CAA-5'\n_____________\|___________________________________\|\n_____________56__________________________________23\n	35 -- 41	37 -- 43	-23.8738 kcal/mol	9.94572 kcal/mol	6.27216 kcal/mol	20 56@LB@ \| \|@LB@5'-GAC...UACCG UU CCGU GUACC C AAGGU...ACA-3'@LB@ UUGCUU GC GAAGCGC GAAGU CGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\|\|:\| :\|\|:\| \|\|\|@LB@ AACGAA CG CUUCGUG UUUUA GCA@LB@3'-UUU...CUUUG UU UU AAUU A AUGUG...CAA-5'@LB@ \| \|@LB@ 56 23@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -23.8738 kcal/mol@LB@Unfolding Energy - mRNA 9.94572 kcal/mol@LB@Unfolding Energy - sRNA 6.27216 kcal/mol@LB@@LB@Position - mRNA 21 -- 55@LB@Position - sRNA 24 -- 55@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 37 -- 43@LB@
122	0.01076	0.2828	b1908	yecA	-7.65	0.074805	79 -- 96	18 -- 40	UPF0149 family protein	_____________78_______________________97\n_____________\|________________________\|\n5'-UAC...UGCCU__A_____________________CUCCU...UGG-3'\n______________GC_ACUUG______UCGUUACACC\n______________\|\|_\|\|\|\|:______\|\|\|\|\|\|\|\|\|\|\n______________CG_UGAAU______AGCAAUGUGG\n3'-UUU...UUCUU________UUUUUA__________UCCUU...CAA-5'\n_____________\|________________________\|\n_____________41_______________________17\n	90 -- 96	18 -- 24	-19.1188 kcal/mol	2.30438 kcal/mol	9.1639 kcal/mol	78 97@LB@ \| \|@LB@5'-UAC...UGCCU A CUCCU...UGG-3'@LB@ GC ACUUG UCGUUACACC@LB@ \|\| \|\|\|\|: \|\|\|\|\|\|\|\|\|\|@LB@ CG UGAAU AGCAAUGUGG@LB@3'-UUU...UUCUU UUUUUA UCCUU...CAA-5'@LB@ \| \|@LB@ 41 17@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -19.1188 kcal/mol@LB@Unfolding Energy - mRNA 2.30438 kcal/mol@LB@Unfolding Energy - sRNA 9.1639 kcal/mol@LB@@LB@Position - mRNA 79 -- 96@LB@Position - sRNA 18 -- 40@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 18 -- 24@LB@
90	0.006331	0.2266	b1710	btuE	-7.57	0.078405	256 -- 270	25 -- 39	glutathione peroxidase	_____________255_____________271\n_____________\|_______________\|\n5'-GCA...GACCA____G__________CCGGU...UCG-3'\n______________CGCU_GAGAAGUUCG\n______________\|:\|\|_:\|:\|\|:\|\|\|\|\n______________GUGA_UUUUUUAAGC\n3'-UUU...UCUUC____A__________AAUGU...CAA-5'\n_____________\|_______________\|\n_____________40______________24\n	264 -- 270	25 -- 31	-13.949 kcal/mol	4.72897 kcal/mol	1.64678 kcal/mol	255 271@LB@ \| \|@LB@5'-GCA...GACCA G CCGGU...UCG-3'@LB@ CGCU GAGAAGUUCG@LB@ \|:\|\| :\|:\|\|:\|\|\|\|@LB@ GUGA UUUUUUAAGC@LB@3'-UUU...UCUUC A AAUGU...CAA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -13.949 kcal/mol@LB@Unfolding Energy - mRNA 4.72897 kcal/mol@LB@Unfolding Energy - sRNA 1.64678 kcal/mol@LB@@LB@Position - mRNA 256 -- 270@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 25 -- 31@LB@
66	0.003432	0.1645	b0882	clpA	-7.45	0.084488	282 -- 290	34 -- 42	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity	_____________281_______291\n_____________\|_________\|\n5'-UUU...CCGUC_________UUACU...CGC-3'\n______________GAGCACUUG\n______________:\|\|\|\|\|\|\|:\n______________UUCGUGAAU\n3'-UUU...CGUUC_________UUUUU...CAA-5'\n_____________\|_________\|\n_____________43________33\n	284 -- 290	34 -- 40	-10.5586 kcal/mol	1.49281 kcal/mol	1.61613 kcal/mol	281 291@LB@ \| \|@LB@5'-UUU...CCGUC UUACU...CGC-3'@LB@ GAGCACUUG@LB@ :\|\|\|\|\|\|\|:@LB@ UUCGUGAAU@LB@3'-UUU...CGUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 43 33@LB@@LB@@LB@Energy -7.45 kcal/mol@LB@Hybridization Energy -10.5586 kcal/mol@LB@Unfolding Energy - mRNA 1.49281 kcal/mol@LB@Unfolding Energy - sRNA 1.61613 kcal/mol@LB@@LB@Position - mRNA 282 -- 290@LB@Position - sRNA 34 -- 42@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 34 -- 40@LB@
188	0.02199	0.3768	b3774	ilvC	-7.43	0.085257	172 -- 181	37 -- 46	ketol-acid reductoisomerase NAD(P)-binding	_____________171________182\n_____________\|__________\|\n5'-AUG...AACAA__________AACAU...GCU-3'\n______________UAAGAAGCAC\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUCUUCGUG\n3'-UUU...AAUUC__________AAUUU...CAA-5'\n_____________\|__________\|\n_____________47_________36\n	175 -- 181	37 -- 43	-13.663 kcal/mol	1.01181 kcal/mol	5.21654 kcal/mol	171 182@LB@ \| \|@LB@5'-AUG...AACAA AACAU...GCU-3'@LB@ UAAGAAGCAC@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUCUUCGUG@LB@3'-UUU...AAUUC AAUUU...CAA-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -7.43 kcal/mol@LB@Hybridization Energy -13.663 kcal/mol@LB@Unfolding Energy - mRNA 1.01181 kcal/mol@LB@Unfolding Energy - sRNA 5.21654 kcal/mol@LB@@LB@Position - mRNA 172 -- 181@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 37 -- 43@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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