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
22	0.0006536	0.09021	b1245	oppC	-8.46	0.045181	270 -- 288	37 -- 58	oligopeptide ABC transporter permease	_____________269____________________289\n_____________\|______________________\|\n5'-GGU...GGCGC_________________C____GUCGA...UUA-3'\n______________AGCUUGU___GGCAGGA_GCAC\n______________\|:\|\|\|\|:___:\|\|\|:\|\|_\|\|\|\|\n______________UUGAACG___UCGUUCU_CGUG\n3'-UUU...CUACU_______AAU_______U____AAUUU...CAA-5'\n_____________\|______________________\|\n_____________59_____________________36\n	277 -- 283	42 -- 48	-22.602 kcal/mol	7.90039 kcal/mol	6.24354 kcal/mol	269 289@LB@ \| \|@LB@5'-GGU...GGCGC C GUCGA...UUA-3'@LB@ AGCUUGU GGCAGGA GCAC@LB@ \|:\|\|\|\|: :\|\|\|:\|\| \|\|\|\|@LB@ UUGAACG UCGUUCU CGUG@LB@3'-UUU...CUACU AAU U AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -22.602 kcal/mol@LB@Unfolding Energy - mRNA 7.90039 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 270 -- 288@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 42 -- 48@LB@
126	0.01159	0.2964	b3693	dgoK	-8.44	0.045823	138 -- 160	34 -- 54	2-oxo-3-deoxygalactonate kinase	_____________137_____________________161\n_____________\|_______________________\|\n5'-CAG...GGCGA___GGCA_______C________CCAUG...CAG-3'\n______________UGC____GAGCAGG_GGCGCUUA\n______________\|\|\|____:\|\|\|\|:\|_:\|\|:\|\|\|\|\n______________ACG____UUCGUUC_UCGUGAAU\n3'-UUU...UUUGA___AA_________U________UUUUU...CAA-5'\n_____________\|_______________________\|\n_____________55______________________33\n	154 -- 160	34 -- 40	-23.026 kcal/mol	8.41527 kcal/mol	6.17478 kcal/mol	137 161@LB@ \| \|@LB@5'-CAG...GGCGA GGCA C CCAUG...CAG-3'@LB@ UGC GAGCAGG GGCGCUUA@LB@ \|\|\| :\|\|\|\|:\| :\|\|:\|\|\|\|@LB@ ACG UUCGUUC UCGUGAAU@LB@3'-UUU...UUUGA AA U UUUUU...CAA-5'@LB@ \| \|@LB@ 55 33@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -23.026 kcal/mol@LB@Unfolding Energy - mRNA 8.41527 kcal/mol@LB@Unfolding Energy - sRNA 6.17478 kcal/mol@LB@@LB@Position - mRNA 138 -- 160@LB@Position - sRNA 34 -- 54@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 34 -- 40@LB@
52	0.002466	0.1527	b3527	yhjJ	-8.40	0.046956	207 -- 220	25 -- 41	putative periplasmic M16 family chaperone	_____________206_______________221\n_____________\|_________________\|\n5'-CUC...UGCAG_________________ACUUU...GGC-3'\n______________GGCAC___AAAAAUUCG\n______________:\|\|\|\|___\|\|\|\|\|\|\|\|\|\n______________UCGUG___UUUUUAAGC\n3'-UUU...GUUCU_____AAU_________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	214 -- 220	25 -- 31	-13.4116 kcal/mol	3.36563 kcal/mol	1.64839 kcal/mol	206 221@LB@ \| \|@LB@5'-CUC...UGCAG ACUUU...GGC-3'@LB@ GGCAC AAAAAUUCG@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCGUG UUUUUAAGC@LB@3'-UUU...GUUCU AAU AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -13.4116 kcal/mol@LB@Unfolding Energy - mRNA 3.36563 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 207 -- 220@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 25 -- 31@LB@
98	0.007325	0.239	b4171	miaA	-8.40	0.046782	42 -- 58	5 -- 24	delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase	_____________41___________________59\n_____________\|____________________\|\n5'-GAA...GUGGA____________________AGCGA...UUU-3'\n______________UUGCAC___GAAAUCUGAUG\n______________\|\|:\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\n______________AAUGUG___CUUUAGACUAC\n3'-UUU...UAAGC______GUC___________ACAA-5'\n_____________\|____________________\|\n_____________25___________________4\n	52 -- 58	5 -- 11	-19.996 kcal/mol	4.00751 kcal/mol	7.58501 kcal/mol	41 59@LB@ \| \|@LB@5'-GAA...GUGGA AGCGA...UUU-3'@LB@ UUGCAC GAAAUCUGAUG@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ AAUGUG CUUUAGACUAC@LB@3'-UUU...UAAGC GUC ACAA-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -19.996 kcal/mol@LB@Unfolding Energy - mRNA 4.00751 kcal/mol@LB@Unfolding Energy - sRNA 7.58501 kcal/mol@LB@@LB@Position - mRNA 42 -- 58@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 5 -- 11@LB@
85	0.005692	0.2157	b4052	dnaB	-8.38	0.047402	89 -- 103	26 -- 40	replicative DNA helicase	_____________88______________104\n_____________\|_______________\|\n5'-UGC...CCACC_______U_______AAUUC...CGG-3'\n______________GUGCUUG_GAAAUUC\n______________\|::\|\|\|:_:\|\|\|\|\|\|\n______________CGUGAAU_UUUUAAG\n3'-UUU...UUCUU_______U_______CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	97 -- 103	26 -- 32	-13.045 kcal/mol	3.01413 kcal/mol	1.64811 kcal/mol	88 104@LB@ \| \|@LB@5'-UGC...CCACC U AAUUC...CGG-3'@LB@ GUGCUUG GAAAUUC@LB@ \|::\|\|\|: :\|\|\|\|\|\|@LB@ CGUGAAU UUUUAAG@LB@3'-UUU...UUCUU U CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -13.045 kcal/mol@LB@Unfolding Energy - mRNA 3.01413 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 89 -- 103@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 26 -- 32@LB@
91	0.006547	0.2317	b1323	tyrR	-8.26	0.051378	202 -- 222	3 -- 23	aromatic amino acid biosynthesis and transport regulon transcriptional regulator; autorepressor; ATPase; phosphatase	_____________201___________________223\n_____________\|_____________________\|\n5'-UCG...UCCCA______U________UU____AAGAC...UUG-3'\n______________UGCGUC_GGAAGUCU__UGUG\n______________\|:\|::\|_\|\|\|\|:\|\|\|__\|\|\|\|\n______________AUGUGG_CCUUUAGA__ACAC\n3'-UUU...AAGCA______U________CU____AA-5'\n_____________\|_____________________\|\n_____________24____________________2\n	209 -- 215	10 -- 16	-19.6247 kcal/mol	3.79223 kcal/mol	7.5769 kcal/mol	201 223@LB@ \| \|@LB@5'-UCG...UCCCA U UU AAGAC...UUG-3'@LB@ UGCGUC GGAAGUCU UGUG@LB@ \|:\|::\| \|\|\|\|:\|\|\| \|\|\|\|@LB@ AUGUGG CCUUUAGA ACAC@LB@3'-UUU...AAGCA U CU AA-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -19.6247 kcal/mol@LB@Unfolding Energy - mRNA 3.79223 kcal/mol@LB@Unfolding Energy - sRNA 7.5769 kcal/mol@LB@@LB@Position - mRNA 202 -- 222@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 10 -- 16@LB@
151	0.0157	0.3349	b0586	entF	-8.26	0.051334	189 -- 199	37 -- 47	enterobactin synthase multienzyme complex component ATP-dependent	_____________188_________200\n_____________\|___________\|\n5'-CCC...CAGUU___________AAUGA...UUG-3'\n______________GCAGGAGGCAC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CGUUCUUCGUG\n3'-UUU...GAAUU___________AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	193 -- 199	37 -- 43	-17.6877 kcal/mol	4.1913 kcal/mol	5.23944 kcal/mol	188 200@LB@ \| \|@LB@5'-CCC...CAGUU AAUGA...UUG-3'@LB@ GCAGGAGGCAC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CGUUCUUCGUG@LB@3'-UUU...GAAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -17.6877 kcal/mol@LB@Unfolding Energy - mRNA 4.1913 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 189 -- 199@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 37 -- 43@LB@
11	0.0001294	0.03789	b3687	ibpA	-8.25	0.051487	69 -- 81	26 -- 38	heat shock chaperone	_____________68____________82\n_____________\|_____________\|\n5'-AAC...AUAAG_____________AUUUC...GCU-3'\n______________GCUUGAAAAGUUC\n______________:\|\|\|:\|\|\|\|:\|\|\|\n______________UGAAUUUUUUAAG\n3'-UUU...CUUCG_____________CAAUG...CAA-5'\n_____________\|_____________\|\n_____________39____________25\n	75 -- 81	26 -- 32	-13.0918 kcal/mol	3.40592 kcal/mol	1.43364 kcal/mol	68 82@LB@ \| \|@LB@5'-AAC...AUAAG AUUUC...GCU-3'@LB@ GCUUGAAAAGUUC@LB@ :\|\|\|:\|\|\|\|:\|\|\|@LB@ UGAAUUUUUUAAG@LB@3'-UUU...CUUCG CAAUG...CAA-5'@LB@ \| \|@LB@ 39 25@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -13.0918 kcal/mol@LB@Unfolding Energy - mRNA 3.40592 kcal/mol@LB@Unfolding Energy - sRNA 1.43364 kcal/mol@LB@@LB@Position - mRNA 69 -- 81@LB@Position - sRNA 26 -- 38@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 26 -- 32@LB@
174	0.01992	0.3669	b1098	tmk	-8.25	0.051647	183 -- 196	29 -- 42	thymidylate kinase	_____________182____________197\n_____________\|______________\|\n5'-UAA...UCUGA______________AAAAA...GCG-3'\n______________AAGUGCUUAAGGAA\n______________\|\|\|::\|\|\|\|\|::\|\|\n______________UUCGUGAAUUUUUU\n3'-UUU...CGUUC______________AAGCA...CAA-5'\n_____________\|______________\|\n_____________43_____________28\n	190 -- 196	29 -- 35	-11.8447 kcal/mol	1.97362 kcal/mol	1.62369 kcal/mol	182 197@LB@ \| \|@LB@5'-UAA...UCUGA AAAAA...GCG-3'@LB@ AAGUGCUUAAGGAA@LB@ \|\|\|::\|\|\|\|\|::\|\|@LB@ UUCGUGAAUUUUUU@LB@3'-UUU...CGUUC AAGCA...CAA-5'@LB@ \| \|@LB@ 43 28@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -11.8447 kcal/mol@LB@Unfolding Energy - mRNA 1.97362 kcal/mol@LB@Unfolding Energy - sRNA 1.62369 kcal/mol@LB@@LB@Position - mRNA 183 -- 196@LB@Position - sRNA 29 -- 42@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 29 -- 35@LB@
198	0.02375	0.3864	b3946	fsaB	-8.18	0.053967	105 -- 117	26 -- 40	fructose-6-phosphate aldolase 2	_____________104_____________118\n_____________\|_______________\|\n5'-UGG...AUCAU_______________CGUAA...CUG-3'\n______________GCAC__GAAGAAUUC\n______________\|\|\|\|__:\|\|:\|\|\|\|\|\n______________CGUG__UUUUUUAAG\n3'-UUU...UUCUU____AA_________CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	111 -- 117	26 -- 32	-11.851 kcal/mol	2.02524 kcal/mol	1.64811 kcal/mol	104 118@LB@ \| \|@LB@5'-UGG...AUCAU CGUAA...CUG-3'@LB@ GCAC GAAGAAUUC@LB@ \|\|\|\| :\|\|:\|\|\|\|\|@LB@ CGUG UUUUUUAAG@LB@3'-UUU...UUCUU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.18 kcal/mol@LB@Hybridization Energy -11.851 kcal/mol@LB@Unfolding Energy - mRNA 2.02524 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 105 -- 117@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 26 -- 32@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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usability assessment

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service.

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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