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
101	0.007657	0.2442	b3928	zapB	-6.83	0.122013	220 -- 239	38 -- 54	FtsZ stabilizer septal ring assembly factor cell division stimulator	_____________219__________________240\n_____________\|____________________\|\n5'-UUU...AGAAG________AAACU_______AAAGU...AAG-3'\n______________UGUUUGAG_____GGAAGCA\n______________\|\|:\|\|:\|\|_____:\|\|\|\|\|\|\n______________ACGAAUUC_____UCUUCGU\n3'-UUU...UUUGA________GU__________GAAUU...CAA-5'\n_____________\|____________________\|\n_____________55___________________37\n	233 -- 239	38 -- 44	-16.6983 kcal/mol	3.7204 kcal/mol	6.15149 kcal/mol	219 240@LB@ \| \|@LB@5'-UUU...AGAAG AAACU AAAGU...AAG-3'@LB@ UGUUUGAG GGAAGCA@LB@ \|\|:\|\|:\|\| :\|\|\|\|\|\|@LB@ ACGAAUUC UCUUCGU@LB@3'-UUU...UUUGA GU GAAUU...CAA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -6.83 kcal/mol@LB@Hybridization Energy -16.6983 kcal/mol@LB@Unfolding Energy - mRNA 3.7204 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 220 -- 239@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 38 -- 44@LB@
125	0.01132	0.2916	b4152	frdC	-8.74	0.037729	137 -- 154	25 -- 41	fumarate reductase (anaerobic) membrane anchor subunit	_____________136________________155\n_____________\|__________________\|\n5'-AGA...AGCAG____AAG___________AAAGA...CGG-3'\n______________GGCA___UAGAAAGUUCG\n______________:\|\|\|___\|\|:\|\|\|:\|\|\|\|\n______________UCGU___AUUUUUUAAGC\n3'-UUU...GUUCU____GA____________AAUGU...CAA-5'\n_____________\|__________________\|\n_____________42_________________24\n	148 -- 154	25 -- 31	-13.3883 kcal/mol	3.00162 kcal/mol	1.64839 kcal/mol	136 155@LB@ \| \|@LB@5'-AGA...AGCAG AAG AAAGA...CGG-3'@LB@ GGCA UAGAAAGUUCG@LB@ :\|\|\| \|\|:\|\|\|:\|\|\|\|@LB@ UCGU AUUUUUUAAGC@LB@3'-UUU...GUUCU GA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -13.3883 kcal/mol@LB@Unfolding Energy - mRNA 3.00162 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 137 -- 154@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 25 -- 31@LB@
159	0.01739	0.3504	b2426	ucpA	-8.50	0.043854	215 -- 229	36 -- 49	furfural resistance protein putative short-chain oxidoreductase	_____________214_____________230\n_____________\|_______________\|\n5'-GUG...CUCAC________C______GAUUA...UAA-3'\n______________GGGCAAGA_AGCACU\n______________::\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UUCGUUCU_UCGUGA\n3'-UUU...ACGAA_______________AUUUU...CAA-5'\n_____________\|_______________\|\n_____________50______________35\n	216 -- 222	42 -- 48	-19.0239 kcal/mol	4.4828 kcal/mol	6.03645 kcal/mol	214 230@LB@ \| \|@LB@5'-GUG...CUCAC C GAUUA...UAA-3'@LB@ GGGCAAGA AGCACU@LB@ ::\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUCGUUCU UCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -19.0239 kcal/mol@LB@Unfolding Energy - mRNA 4.4828 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 215 -- 229@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 42 -- 48@LB@
153	0.016	0.3359	b2167	fruA	-4.10	0.476180	191 -- 199	37 -- 45	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________190_______200\n_____________\|_________\|\n5'-CGC...AGCAG_________AAUGA...AAA-3'\n______________GAGAGGCAU\n______________:\|\|\|:\|\|\|:\n______________UUCUUCGUG\n3'-UUU...AUUCG_________AAUUU...CAA-5'\n_____________\|_________\|\n_____________46________36\n	193 -- 199	37 -- 43	-10.9543 kcal/mol	1.97714 kcal/mol	4.8783 kcal/mol	190 200@LB@ \| \|@LB@5'-CGC...AGCAG AAUGA...AAA-3'@LB@ GAGAGGCAU@LB@ :\|\|\|:\|\|\|:@LB@ UUCUUCGUG@LB@3'-UUU...AUUCG AAUUU...CAA-5'@LB@ \| \|@LB@ 46 36@LB@@LB@@LB@Energy -4.10 kcal/mol@LB@Hybridization Energy -10.9543 kcal/mol@LB@Unfolding Energy - mRNA 1.97714 kcal/mol@LB@Unfolding Energy - sRNA 4.8783 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 37 -- 45@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 37 -- 43@LB@
58	0.002968	0.1645	b0421	ispA	-9.70	0.019970	54 -- 76	25 -- 47	geranyltranstransferase	_____________53______________________77\n_____________\|_______________________\|\n5'-CUG...CCGCU_G__________GAAC_______AACGC...UCG-3'\n______________G_AAGAGGCGCU____GAGUUCG\n______________\|_\|\|\|\|:\|\|:\|\|____:\|:\|\|\|\|\n______________C_UUCUUCGUGA____UUUAAGC\n3'-UUU...GAAUU_G__________AUUU_______AAUGU...CAA-5'\n_____________\|_______________________\|\n_____________48______________________24\n	70 -- 76	25 -- 31	-22.3845 kcal/mol	6.43631 kcal/mol	6.25056 kcal/mol	53 77@LB@ \| \|@LB@5'-CUG...CCGCU G GAAC AACGC...UCG-3'@LB@ G AAGAGGCGCU GAGUUCG@LB@ \| \|\|\|\|:\|\|:\|\| :\|:\|\|\|\|@LB@ C UUCUUCGUGA UUUAAGC@LB@3'-UUU...GAAUU G AUUU AAUGU...CAA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -22.3845 kcal/mol@LB@Unfolding Energy - mRNA 6.43631 kcal/mol@LB@Unfolding Energy - sRNA 6.25056 kcal/mol@LB@@LB@Position - mRNA 54 -- 76@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 25 -- 31@LB@
2	4.936e-07	0.0007949	b1237	hns	-13.24	0.001473	195 -- 222	26 -- 57	global DNA-binding transcriptional dual regulator H-NS	_____________194______________________________223\n_____________\|________________________________\|\n5'-CUC...AGAUU___ACAA_________________________UGAAC...UAG-3'\n______________ACU____UGAGC__GAAGCACUUAAA__AUUC\n______________\|\|\|____\|:\|\|\|__\|\|\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UGA____AUUCG__CUUCGUGAAUUU__UAAG\n3'-UUU...UACUU___ACGA_____UU____________UU____CAAUG...CAA-5'\n_____________\|________________________________\|\n_____________58_______________________________25\n	212 -- 218	32 -- 38	-22.6274 kcal/mol	3.10903 kcal/mol	6.27605 kcal/mol	194 223@LB@ \| \|@LB@5'-CUC...AGAUU ACAA UGAAC...UAG-3'@LB@ ACU UGAGC GAAGCACUUAAA AUUC@LB@ \|\|\| \|:\|\|\| \|\|\|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UGA AUUCG CUUCGUGAAUUU UAAG@LB@3'-UUU...UACUU ACGA UU UU CAAUG...CAA-5'@LB@ \| \|@LB@ 58 25@LB@@LB@@LB@Energy -13.24 kcal/mol@LB@Hybridization Energy -22.6274 kcal/mol@LB@Unfolding Energy - mRNA 3.10903 kcal/mol@LB@Unfolding Energy - sRNA 6.27605 kcal/mol@LB@@LB@Position - mRNA 195 -- 222@LB@Position - sRNA 26 -- 57@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 32 -- 38@LB@
94	0.006975	0.2379	b1284	yciT	-8.66	0.039674	34 -- 64	15 -- 42	global regulator of transcription; DeoR family	_____________33_______________________________65\n_____________\|________________________________\|\n5'-GCA...AUCUC___A________GCA___C_____________UUGCU...CCA-3'\n______________GAG_UACUUAAA___GAA_UC_UUGCGCCAGG\n______________:\|\|_:\|\|\|\|\|\|\|___:\|\|_\|\|_\|\|:\|:\|\|\|\|\|\n______________UUC_GUGAAUUU___UUU_AG_AAUGUGGUCC\n3'-UUU...CGUUC__________________A__C__________UUUAG...CAA-5'\n_____________\|________________________________\|\n_____________43_______________________________14\n	58 -- 64	15 -- 21	-23.4161 kcal/mol	5.55126 kcal/mol	9.20431 kcal/mol	33 65@LB@ \| \|@LB@5'-GCA...AUCUC A GCA C UUGCU...CCA-3'@LB@ GAG UACUUAAA GAA UC UUGCGCCAGG@LB@ :\|\| :\|\|\|\|\|\|\| :\|\| \|\| \|\|:\|:\|\|\|\|\|@LB@ UUC GUGAAUUU UUU AG AAUGUGGUCC@LB@3'-UUU...CGUUC A C UUUAG...CAA-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -23.4161 kcal/mol@LB@Unfolding Energy - mRNA 5.55126 kcal/mol@LB@Unfolding Energy - sRNA 9.20431 kcal/mol@LB@@LB@Position - mRNA 34 -- 64@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 15 -- 21@LB@
162	0.01764	0.3508	b0654	gltJ	-6.81	0.123116	18 -- 45	15 -- 42	glutamate/aspartate ABC transporter permease	_____________17___________________________46\n_____________\|____________________________\|\n5'-CAA...UGACA_______GAACU____ACAAGA______GGCGG...UCG-3'\n______________AGGCACU_____AAUU______ACCAGG\n______________\|:\|\|\|\|\|_____\|\|\|\|______\|\|\|\|\|\|\n______________UUCGUGA_____UUAA______UGGUCC\n3'-UUU...CGUUC_______AUUUU____GCAAUG______UUUAG...CAA-5'\n_____________\|____________________________\|\n_____________43___________________________14\n	18 -- 24	36 -- 42	-19.3193 kcal/mol	3.30421 kcal/mol	9.20431 kcal/mol	17 46@LB@ \| \|@LB@5'-CAA...UGACA GAACU ACAAGA GGCGG...UCG-3'@LB@ AGGCACU AAUU ACCAGG@LB@ \|:\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ UUCGUGA UUAA UGGUCC@LB@3'-UUU...CGUUC AUUUU GCAAUG UUUAG...CAA-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -19.3193 kcal/mol@LB@Unfolding Energy - mRNA 3.30421 kcal/mol@LB@Unfolding Energy - sRNA 9.20431 kcal/mol@LB@@LB@Position - mRNA 18 -- 45@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 36 -- 42@LB@
118	0.009927	0.271	b1654	grxD	-11.37	0.006167	180 -- 241	7 -- 60	glutaredoxin-4	_____________179_______________________________________________________________242\n_____________\|_________________________________________________________________\|\n5'-AAA...GUAAA________AGG________CAAUG_____CACUAUCG_______C_A_________AUUG_____AAACC...CUG-3'\n______________GAAGUUUG___AAGCAAGA_____AGCAC________AAAAAAU_C___ACGCCAG_____CUGA\n______________\|\|\|::\|\|\|___\|\|\|\|\|\|\|\|_____\|\|\|\|\|________\|\|\|\|\|\|\|_\|___\|\|:\|\|\|\|_____\|\|\|\|\n______________CUUUGAAC___UUCGUUCU_____UCGUG________UUUUUUA_G___UGUGGUC_____GACU\n3'-UUU...CCCUA________GAA__________________AA_____________A_CAA_______CUUUA____ACACAA-5'\n_____________\|_________________________________________________________________\|\n_____________61________________________________________________________________6\n	227 -- 233	16 -- 22	-34.247 kcal/mol	9.03509 kcal/mol	13.8468 kcal/mol	179 242@LB@ \| \|@LB@5'-AAA...GUAAA AGG CAAUG CACUAUCG C A AUUG AAACC...CUG-3'@LB@ GAAGUUUG AAGCAAGA AGCAC AAAAAAU C ACGCCAG CUGA@LB@ \|\|\|::\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| \| \|\|:\|\|\|\| \|\|\|\|@LB@ CUUUGAAC UUCGUUCU UCGUG UUUUUUA G UGUGGUC GACU@LB@3'-UUU...CCCUA GAA AA A CAA CUUUA ACACAA-5'@LB@ \| \|@LB@ 61 6@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -34.247 kcal/mol@LB@Unfolding Energy - mRNA 9.03509 kcal/mol@LB@Unfolding Energy - sRNA 13.8468 kcal/mol@LB@@LB@Position - mRNA 180 -- 241@LB@Position - sRNA 7 -- 60@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 16 -- 22@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@

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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