Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
179	0.01766	0.3104	b0377	sbmA	-9.49	0.147268	6 -- 15	3 -- 12	peptide antibiotic transporter	b1496	_____________5__________16\n_____________\|__________\|\n______5'-GAUCC_______G__AAUCC...ACU-3'\n______________UGCGCGU_UU\n______________\|\|\|\|\|\|\|_\|\|\n______________ACGCGCA_AA\n3'-UUU...UGUUU_______G__AG-5'\n_____________\|__________\|\n_____________13_________2\n	6 -- 12	6 -- 12	-14.1156 kcal/mol	3.45883 kcal/mol	1.16529 kcal/mol	5 16@LB@ \| \|@LB@ 5'-GAUCC G AAUCC...ACU-3'@LB@ UGCGCGU UU@LB@ \|\|\|\|\|\|\| \|\|@LB@ ACGCGCA AA@LB@3'-UUU...UGUUU G AG-5'@LB@ \| \|@LB@ 13 2@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -14.1156 kcal/mol@LB@Unfolding Energy - mRNA 3.45883 kcal/mol@LB@Unfolding Energy - sRNA 1.16529 kcal/mol@LB@@LB@Position - mRNA 6 -- 15@LB@Position - sRNA 3 -- 12@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 6 -- 12@LB@
17	0.0005644	0.1124	b0949	uup	-13.14	0.034258	282 -- 297	4 -- 21	replication regulatory ABC-F family DNA-binding ATPase		_____________281________________298\n_____________\|__________________\|\n5'-GAU...UCGAA__________________GUC-3'\n______________GAUAACGAA__CGUGUUU\n______________\|\|\|\|\|\|:\|\|__\|\|:\|\|:\|\n______________CUAUUGUUU__GCGCAGA\n3'-UUU...UACUA_________AC_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	291 -- 297	4 -- 10	-16.3224 kcal/mol	1.92683 kcal/mol	1.2552 kcal/mol	281 298@LB@ \| \|@LB@5'-GAU...UCGAA GUC-3'@LB@ GAUAACGAA CGUGUUU@LB@ \|\|\|\|\|\|:\|\| \|\|:\|\|:\|@LB@ CUAUUGUUU GCGCAGA@LB@3'-UUU...UACUA AC AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 1.92683 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 282 -- 297@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 4 -- 10@LB@
19	0.0006629	0.1181	b2909	ygfB	-11.13	0.077732	186 -- 206	4 -- 22	UPF0149 family protein		_____________185___________________207\n_____________\|_____________________\|\n5'-AAA...CCCUU___C_________UUA_____AUACA...UCA-3'\n______________UGA_GACGAAUGC___UGUCU\n______________\|\|\|_:\|\|:\|\|\|\|\|___:\|\|\|\|\n______________ACU_UUGUUUACG___GCAGA\n3'-UUU...CUACU___A_________C_______AAG-5'\n_____________\|_____________________\|\n_____________23____________________3\n	192 -- 198	10 -- 16	-17.2827 kcal/mol	4.89762 kcal/mol	1.2572 kcal/mol	185 207@LB@ \| \|@LB@5'-AAA...CCCUU C UUA AUACA...UCA-3'@LB@ UGA GACGAAUGC UGUCU@LB@ \|\|\| :\|\|:\|\|\|\|\| :\|\|\|\|@LB@ ACU UUGUUUACG GCAGA@LB@3'-UUU...CUACU A C AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -17.2827 kcal/mol@LB@Unfolding Energy - mRNA 4.89762 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 186 -- 206@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 10 -- 16@LB@
47	0.003448	0.2484	b0614	citX	-10.13	0.115098	76 -- 91	4 -- 17	apo-citrate lyase phosphoribosyl-dephospho-CoA transferase		_____________75_______________92\n_____________\|________________\|\n5'-UUA...GCUGC____AC__________GCUGA...UCA-3'\n______________GCGA__GUGCGCGUCU\n______________:\|:\|__:\|\|\|\|\|\|\|\|\|\n______________UGUU__UACGCGCAGA\n3'-UUU...ACUAU________________AAG-5'\n_____________\|________________\|\n_____________18_______________3\n	85 -- 91	4 -- 10	-19.1919 kcal/mol	7.83057 kcal/mol	1.22888 kcal/mol	75 92@LB@ \| \|@LB@5'-UUA...GCUGC AC GCUGA...UCA-3'@LB@ GCGA GUGCGCGUCU@LB@ :\|:\| :\|\|\|\|\|\|\|\|\|@LB@ UGUU UACGCGCAGA@LB@3'-UUU...ACUAU AAG-5'@LB@ \| \|@LB@ 18 3@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -19.1919 kcal/mol@LB@Unfolding Energy - mRNA 7.83057 kcal/mol@LB@Unfolding Energy - sRNA 1.22888 kcal/mol@LB@@LB@Position - mRNA 76 -- 91@LB@Position - sRNA 4 -- 17@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 4 -- 10@LB@
49	0.004401	0.299	b0093	ftsQ	-10.19	0.112476	259 -- 274	4 -- 20	divisome assembly protein membrane anchored protein involved in growth of wall at septum		_____________258_______________275\n_____________\|_________________\|\n5'-GCU...CCGCA________A________GGCGG...CCG-3'\n______________AUAAUGGA__CGCGUCU\n______________\|\|\|\|:::\|__\|\|\|\|\|\|\|\n______________UAUUGUUU__GCGCAGA\n3'-UUU...ACUAC________AC_______AAG-5'\n_____________\|_________________\|\n_____________21________________3\n	268 -- 274	4 -- 10	-13.8485 kcal/mol	2.40331 kcal/mol	1.25368 kcal/mol	258 275@LB@ \| \|@LB@5'-GCU...CCGCA A GGCGG...CCG-3'@LB@ AUAAUGGA CGCGUCU@LB@ \|\|\|\|:::\| \|\|\|\|\|\|\|@LB@ UAUUGUUU GCGCAGA@LB@3'-UUU...ACUAC AC AAG-5'@LB@ \| \|@LB@ 21 3@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -13.8485 kcal/mol@LB@Unfolding Energy - mRNA 2.40331 kcal/mol@LB@Unfolding Energy - sRNA 1.25368 kcal/mol@LB@@LB@Position - mRNA 259 -- 274@LB@Position - sRNA 4 -- 20@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 4 -- 10@LB@
60	0.00555	0.3084	b2062	wza	-10.85	0.086669	18 -- 25	4 -- 11	colanic acid export protein; outer membrane auxillary lipoprotein		_____________17_______26\n_____________\|________\|\n5'-AAA...CGGUA________GGAUG...GCA-3'\n______________GCGUGUCU\n______________\|\|\|:\|\|\|\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	19 -- 25	4 -- 10	-13.9362 kcal/mol	1.92535 kcal/mol	1.15639 kcal/mol	17 26@LB@ \| \|@LB@5'-AAA...CGGUA GGAUG...GCA-3'@LB@ GCGUGUCU@LB@ \|\|\|:\|\|\|\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -13.9362 kcal/mol@LB@Unfolding Energy - mRNA 1.92535 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 18 -- 25@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 4 -- 10@LB@
63	0.0059	0.3087	b3834	ubiJ	-8.76	0.193647	289 -- 295	4 -- 10	aerobic ubiquinone synthesis protein SCP2 family protein		_____________288_____296\n_____________\|_______\|\n5'-GCU...CCGCU_______GCUGG-3'\n______________CGCGUCU\n______________\|\|\|\|\|\|\|\n______________GCGCAGA\n3'-UUU...UUUAC_______AAG-5'\n_____________\|_______\|\n_____________11______3\n	289 -- 295	4 -- 10	-11.2085 kcal/mol	1.2993 kcal/mol	1.14958 kcal/mol	288 296@LB@ \| \|@LB@5'-GCU...CCGCU GCUGG-3'@LB@ CGCGUCU@LB@ \|\|\|\|\|\|\|@LB@ GCGCAGA@LB@3'-UUU...UUUAC AAG-5'@LB@ \| \|@LB@ 11 3@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.2085 kcal/mol@LB@Unfolding Energy - mRNA 1.2993 kcal/mol@LB@Unfolding Energy - sRNA 1.14958 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 4 -- 10@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 4 -- 10@LB@
68	0.006348	0.3087	b1202	ycgV	-6.40	0.429936	233 -- 244	4 -- 18	putative adhesin	b2647	_____________232_____________245\n_____________\|_______________\|\n5'-ACU...ACCAA_______________CGCUG...UUG-3'\n______________AGCAGAU___CGUCU\n______________\|:\|\|:\|\|___\|\|\|\|\|\n______________UUGUUUA___GCAGA\n3'-UUU...UACUA_______CGC_____AAG-5'\n_____________\|_______________\|\n_____________19______________3\n	233 -- 239	12 -- 18	-9.8712 kcal/mol	2.23703 kcal/mol	1.22995 kcal/mol	232 245@LB@ \| \|@LB@5'-ACU...ACCAA CGCUG...UUG-3'@LB@ AGCAGAU CGUCU@LB@ \|:\|\|:\|\| \|\|\|\|\|@LB@ UUGUUUA GCAGA@LB@3'-UUU...UACUA CGC AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -9.8712 kcal/mol@LB@Unfolding Energy - mRNA 2.23703 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 233 -- 244@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 12 -- 18@LB@
69	0.006491	0.3087	b3347	fkpA	-11.66	0.062814	96 -- 113	4 -- 22	FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)		_____________95__________________114\n_____________\|___________________\|\n5'-UGG...AUAGA___________________GUAUG...CAG-3'\n______________UGAUAAUAGG_GCGUGUCU\n______________\|\|\|\|\|\|:\|::_\|\|\|:\|\|\|\|\n______________ACUAUUGUUU_CGCGCAGA\n3'-UUU...CUACU__________A________AAG-5'\n_____________\|___________________\|\n_____________23__________________3\n	107 -- 113	4 -- 10	-21.7718 kcal/mol	8.85627 kcal/mol	1.2572 kcal/mol	95 114@LB@ \| \|@LB@5'-UGG...AUAGA GUAUG...CAG-3'@LB@ UGAUAAUAGG GCGUGUCU@LB@ \|\|\|\|\|\|:\|:: \|\|\|:\|\|\|\|@LB@ ACUAUUGUUU CGCGCAGA@LB@3'-UUU...CUACU A AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -21.7718 kcal/mol@LB@Unfolding Energy - mRNA 8.85627 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 96 -- 113@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 4 -- 10@LB@
81	0.007385	0.3087	b0736	ybgC	-11.71	0.061637	220 -- 237	4 -- 21	acyl-CoA thioester hydrolase		_____________219________________238\n_____________\|__________________\|\n5'-UUG...GUUUC______C___U_______ACUAU...AAA-3'\n______________GAUGGC_GGU_CGCGUCU\n______________\|\|\|::\|_::\|_\|\|\|\|\|\|\|\n______________CUAUUG_UUA_GCGCAGA\n3'-UUU...UACUA______U___C_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	231 -- 237	4 -- 10	-19.027 kcal/mol	6.06673 kcal/mol	1.2552 kcal/mol	219 238@LB@ \| \|@LB@5'-UUG...GUUUC C U ACUAU...AAA-3'@LB@ GAUGGC GGU CGCGUCU@LB@ \|\|\|::\| ::\| \|\|\|\|\|\|\|@LB@ CUAUUG UUA GCGCAGA@LB@3'-UUU...UACUA U C AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -19.027 kcal/mol@LB@Unfolding Energy - mRNA 6.06673 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 220 -- 237@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 4 -- 10@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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