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	Additional homologs
6	4.032e-05	0.02042	b0889	lrp	-10.51	0.011361	210 -- 221	37 -- 48	leucine-responsive global transcriptional regulator		_____________209__________222\n_____________\|____________\|\n5'-GUG...UAGAU____________CCUGG...AGC-3'\n______________AGCAAGAAGCGC\n______________\|\|\|\|\|\|\|\|\|\|:\|\n______________UCGUUCUUCGUG\n3'-UUU...CGAAU____________AAUUU...CAA-5'\n_____________\|____________\|\n_____________49___________36\n	215 -- 221	37 -- 43	-19.5953 kcal/mol	3.24674 kcal/mol	5.83483 kcal/mol	209 222@LB@ \| \|@LB@5'-GUG...UAGAU CCUGG...AGC-3'@LB@ AGCAAGAAGCGC@LB@ \|\|\|\|\|\|\|\|\|\|:\|@LB@ UCGUUCUUCGUG@LB@3'-UUU...CGAAU AAUUU...CAA-5'@LB@ \| \|@LB@ 49 36@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -19.5953 kcal/mol@LB@Unfolding Energy - mRNA 3.24674 kcal/mol@LB@Unfolding Energy - sRNA 5.83483 kcal/mol@LB@@LB@Position - mRNA 210 -- 221@LB@Position - sRNA 37 -- 48@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 37 -- 43@LB@
103	0.00845	0.2642	b0936	ssuA	-4.91	0.333979	11 -- 31	10 -- 40	aliphatic sulfonate ABC transporter periplasmic binding protein		_____________10______________________________32\n_____________\|_______________________________\|\n5'-AGU...UAAGC_______________________________CUGCA...AUC-3'\n______________GCAC_UGAAA________GC_UCAGGAGAUC\n______________\|\|\|\|_\|:\|\|\|________:\|_:\|\|\|\|\|:\|\|\|\n______________CGUG_AUUUU________UG_GGUCCUUUAG\n3'-UUU...UUCUU____A_____UUAAGCAA__U__________ACUAC...CAA-5'\n_____________\|_______________________________\|\n_____________41______________________________9\n	25 -- 31	10 -- 16	-20.0893 kcal/mol	5.95403 kcal/mol	9.22048 kcal/mol	10 32@LB@ \| \|@LB@5'-AGU...UAAGC CUGCA...AUC-3'@LB@ GCAC UGAAA GC UCAGGAGAUC@LB@ \|\|\|\| \|:\|\|\| :\| :\|\|\|\|\|:\|\|\|@LB@ CGUG AUUUU UG GGUCCUUUAG@LB@3'-UUU...UUCUU A UUAAGCAA U ACUAC...CAA-5'@LB@ \| \|@LB@ 41 9@LB@@LB@@LB@Energy -4.91 kcal/mol@LB@Hybridization Energy -20.0893 kcal/mol@LB@Unfolding Energy - mRNA 5.95403 kcal/mol@LB@Unfolding Energy - sRNA 9.22048 kcal/mol@LB@@LB@Position - mRNA 11 -- 31@LB@Position - sRNA 10 -- 40@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 10 -- 16@LB@
104	0.008606	0.2665	b0956	matP	-4.56	0.392859	215 -- 228	25 -- 38	Ter macrodomain organizer matS-binding protein		_____________214____________229\n_____________\|______________\|\n5'-UUU...CAACA_________UC___AAAGC...AAG-3'\n______________ACUUGAAAA__UUG\n______________\|\|\|\|:\|\|\|\|__\|:\|\n______________UGAAUUUUU__AGC\n3'-UUU...CUUCG_________UA___AAUGU...CAA-5'\n_____________\|______________\|\n_____________39_____________24\n	216 -- 222	31 -- 37	-8.38693 kcal/mol	2.39574 kcal/mol	1.4343 kcal/mol	214 229@LB@ \| \|@LB@5'-UUU...CAACA UC AAAGC...AAG-3'@LB@ ACUUGAAAA UUG@LB@ \|\|\|\|:\|\|\|\| \|:\|@LB@ UGAAUUUUU AGC@LB@3'-UUU...CUUCG UA AAUGU...CAA-5'@LB@ \| \|@LB@ 39 24@LB@@LB@@LB@Energy -4.56 kcal/mol@LB@Hybridization Energy -8.38693 kcal/mol@LB@Unfolding Energy - mRNA 2.39574 kcal/mol@LB@Unfolding Energy - sRNA 1.4343 kcal/mol@LB@@LB@Position - mRNA 215 -- 228@LB@Position - sRNA 25 -- 38@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 31 -- 37@LB@
81	0.005437	0.2146	b1073	flgB	-5.23	0.286610	229 -- 247	36 -- 53	flagellar component of cell-proximal portion of basal-body rod		_____________228_________________248\n_____________\|___________________\|\n5'-UGA...CUUAC____UCAA___________CAAUC...CCG-3'\n______________GUUU____CAAGAGGCGCU\n______________\|:\|\|____\|\|\|\|\|:\|\|:\|\|\n______________CGAA____GUUCUUCGUGA\n3'-UUU...UUGAA____UUC____________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________35\n	241 -- 247	36 -- 42	-18.0666 kcal/mol	6.73003 kcal/mol	6.10238 kcal/mol	228 248@LB@ \| \|@LB@5'-UGA...CUUAC UCAA CAAUC...CCG-3'@LB@ GUUU CAAGAGGCGCU@LB@ \|:\|\| \|\|\|\|\|:\|\|:\|\|@LB@ CGAA GUUCUUCGUGA@LB@3'-UUU...UUGAA UUC AUUUU...CAA-5'@LB@ \| \|@LB@ 54 35@LB@@LB@@LB@Energy -5.23 kcal/mol@LB@Hybridization Energy -18.0666 kcal/mol@LB@Unfolding Energy - mRNA 6.73003 kcal/mol@LB@Unfolding Energy - sRNA 6.10238 kcal/mol@LB@@LB@Position - mRNA 229 -- 247@LB@Position - sRNA 36 -- 53@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 36 -- 42@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@
170	0.01916	0.363	b1202	ycgV	-6.78	0.125661	82 -- 88	39 -- 45	putative adhesin	b2647	_____________81______89\n_____________\|_______\|\n5'-ACU...UCUCU_______UCAUC...UUG-3'\n______________GAGAAGC\n______________:\|\|\|\|\|\|\n______________UUCUUCG\n3'-UUU...AUUCG_______UGAAU...CAA-5'\n_____________\|_______\|\n_____________46______38\n	82 -- 88	39 -- 45	-7.60605 kcal/mol	0.31609 kcal/mol	0.514773 kcal/mol	81 89@LB@ \| \|@LB@5'-ACU...UCUCU UCAUC...UUG-3'@LB@ GAGAAGC@LB@ :\|\|\|\|\|\|@LB@ UUCUUCG@LB@3'-UUU...AUUCG UGAAU...CAA-5'@LB@ \| \|@LB@ 46 38@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -7.60605 kcal/mol@LB@Unfolding Energy - mRNA 0.31609 kcal/mol@LB@Unfolding Energy - sRNA 0.514773 kcal/mol@LB@@LB@Position - mRNA 82 -- 88@LB@Position - sRNA 39 -- 45@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 39 -- 45@LB@
59	0.003153	0.1645	b1220	ychO	-8.71	0.038404	242 -- 262	37 -- 56	putative invasin		_____________241___________________263\n_____________\|_____________________\|\n5'-UCA...UUACU________U______C_____AGCUA...CAA-3'\n______________CUUGCUUG_AGCAGG_GGUAC\n______________\|\|\|\|\|\|\|:_\|\|\|\|:\|_:\|:\|\|\n______________GAACGAAU_UCGUUC_UCGUG\n3'-UUU...ACUUU_______________U_____AAUUU...CAA-5'\n_____________\|_____________________\|\n_____________57____________________36\n	242 -- 248	50 -- 56	-24.8668 kcal/mol	9.95535 kcal/mol	6.20049 kcal/mol	241 263@LB@ \| \|@LB@5'-UCA...UUACU U C AGCUA...CAA-3'@LB@ CUUGCUUG AGCAGG GGUAC@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\| :\|:\|\|@LB@ GAACGAAU UCGUUC UCGUG@LB@3'-UUU...ACUUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -24.8668 kcal/mol@LB@Unfolding Energy - mRNA 9.95535 kcal/mol@LB@Unfolding Energy - sRNA 6.20049 kcal/mol@LB@@LB@Position - mRNA 242 -- 262@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 50 -- 56@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@
73	0.004067	0.1794	b1244	oppB	-5.52	0.247965	106 -- 113	36 -- 43	oligopeptide ABC transporter permease		_____________105______114\n_____________\|________\|\n5'-UCC...AUUGU________AAUGG...GCC-3'\n______________GAAGCACU\n______________\|\|\|\|\|\|\|\|\n______________CUUCGUGA\n3'-UUU...UCGUU________AUUUU...CAA-5'\n_____________\|________\|\n_____________44_______35\n	107 -- 113	36 -- 42	-11.7212 kcal/mol	2.50266 kcal/mol	3.69444 kcal/mol	105 114@LB@ \| \|@LB@5'-UCC...AUUGU AAUGG...GCC-3'@LB@ GAAGCACU@LB@ \|\|\|\|\|\|\|\|@LB@ CUUCGUGA@LB@3'-UUU...UCGUU AUUUU...CAA-5'@LB@ \| \|@LB@ 44 35@LB@@LB@@LB@Energy -5.52 kcal/mol@LB@Hybridization Energy -11.7212 kcal/mol@LB@Unfolding Energy - mRNA 2.50266 kcal/mol@LB@Unfolding Energy - sRNA 3.69444 kcal/mol@LB@@LB@Position - mRNA 106 -- 113@LB@Position - sRNA 36 -- 43@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 36 -- 42@LB@
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@

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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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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