Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
16	0.0006527	0.1243	b2563	acpS	-16.60	0.010715	145 -- 164	1 -- 23	holo-[acyl-carrier-protein] synthase 1		_____________144_____________________165\n_____________\|_______________________\|\n5'-GCC...UGACC______G_____U__________AGAAA...GCG-3'\n______________GGAC_U_AAAGA___GCGGUGGC\n______________\|\|\|\|_\|_\|\|\|\|\|___\|\|:\|\|\|\|\|\n______________CCUG_A_UUUCU___CGUCACCG\n3'-UUU...UUACC____U_G_____UUU________-5'\n_____________\|______________________\|\n_____________24_____________________1\n	158 -- 164	1 -- 7	-25.7246 kcal/mol	7.54829 kcal/mol	1.57928 kcal/mol	144 165@LB@ \| \|@LB@5'-GCC...UGACC G U AGAAA...GCG-3'@LB@ GGAC U AAAGA GCGGUGGC@LB@ \|\|\|\| \| \|\|\|\|\| \|\|:\|\|\|\|\|@LB@ CCUG A UUUCU CGUCACCG@LB@3'-UUU...UUACC U G UUU -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -16.60 kcal/mol@LB@Hybridization Energy -25.7246 kcal/mol@LB@Unfolding Energy - mRNA 7.54829 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 145 -- 164@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 1 -- 7@LB@
195	0.01413	0.2529	b2527	hscB	-14.38	0.038945	62 -- 81	1 -- 21	HscA co-chaperone J domain-containing protein Hsc56; IscU-specific chaperone HscAB		_____________61____________________82\n_____________\|_____________________\|\n5'-GGU...CCCGA__________U__________UGCGG...CUG-3'\n______________ACGUCAAAGA_GAGU_GUGGU\n______________\|\|:\|\|\|\|\|\|\|_:\|\|:_\|\|\|\|:\n______________UGUAGUUUCU_UUCG_CACCG\n3'-UUU...ACCCC__________U____U_____-5'\n_____________\|____________________\|\n_____________22___________________1\n	65 -- 71	12 -- 18	-23.3701 kcal/mol	7.47956 kcal/mol	1.51103 kcal/mol	61 82@LB@ \| \|@LB@5'-GGU...CCCGA U UGCGG...CUG-3'@LB@ ACGUCAAAGA GAGU GUGGU@LB@ \|\|:\|\|\|\|\|\|\| :\|\|: \|\|\|\|:@LB@ UGUAGUUUCU UUCG CACCG@LB@3'-UUU...ACCCC U U -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.38 kcal/mol@LB@Hybridization Energy -23.3701 kcal/mol@LB@Unfolding Energy - mRNA 7.47956 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 62 -- 81@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 12 -- 18@LB@
9	0.0002541	0.09908	b4000	hupA	-15.77	0.017828	82 -- 110	1 -- 35	HU DNA-binding transcriptional regulator alpha subunit		_____________81__________________________________111\n_____________\|___________________________________\|\n5'-UUU...UCUGG______UUUG_________________AA______UAUCG...CUG-3'\n______________UCUACA____GGGGGCG______AAAA__AGUGGC\n______________\|\|:\|\|\|____\|\|\|\|:\|:______\|\|\|\|__\|\|\|\|\|\|\n______________AGGUGU____CCCCUGU______UUUU__UCACCG\n3'-UUU...ACCCG______UUUA_______AGUUUC____CG______-5'\n_____________\|__________________________________\|\n_____________36_________________________________1\n	92 -- 98	19 -- 25	-28.6527 kcal/mol	7.84855 kcal/mol	5.03645 kcal/mol	81 111@LB@ \| \|@LB@5'-UUU...UCUGG UUUG AA UAUCG...CUG-3'@LB@ UCUACA GGGGGCG AAAA AGUGGC@LB@ \|\|:\|\|\| \|\|\|\|:\|: \|\|\|\| \|\|\|\|\|\|@LB@ AGGUGU CCCCUGU UUUU UCACCG@LB@3'-UUU...ACCCG UUUA AGUUUC CG -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -28.6527 kcal/mol@LB@Unfolding Energy - mRNA 7.84855 kcal/mol@LB@Unfolding Energy - sRNA 5.03645 kcal/mol@LB@@LB@Position - mRNA 82 -- 110@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 19 -- 25@LB@
20	0.0007622	0.1243	b1507	hipA	-19.17	0.001718	1 -- 29	1 -- 31	inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase		______________1________________________________30\n______________\|________________________________\|\n___________5'-________CU___________C___________GAAAA...UAG-3'\n______________CAAAAUGG__GGACG_CAGAG__GAGC__UGGC\n______________\|\|\|\|\|\|\|\|__\|\|\|\|:_\|\|:\|\|__:\|\|\|__\|\|\|\|\n______________GUUUUACC__CCUGU_GUUUC__UUCG__ACCG\n3'-UUU...GAGGU_______________A_____UU____UC____-5'\n_____________\|________________________________\|\n_____________32_______________________________1\n	2 -- 8	24 -- 30	-30.0086 kcal/mol	8.29611 kcal/mol	2.53929 kcal/mol	1 30@LB@ \| \|@LB@ 5'- CU C GAAAA...UAG-3'@LB@ CAAAAUGG GGACG CAGAG GAGC UGGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|: \|\|:\|\| :\|\|\| \|\|\|\|@LB@ GUUUUACC CCUGU GUUUC UUCG ACCG@LB@3'-UUU...GAGGU A UU UC -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -19.17 kcal/mol@LB@Hybridization Energy -30.0086 kcal/mol@LB@Unfolding Energy - mRNA 8.29611 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 1 -- 29@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 2 -- 8@LB@Position Seed - sRNA 24 -- 30@LB@
128	0.00928	0.2491	b0491	fetB	-12.70	0.090276	178 -- 195	1 -- 17	iron export ABC transporter permease; peroxide resistance protein		_____________177________________196\n_____________\|__________________\|\n5'-GCC...CAUGC________U____GAA__ACGCU...AGA-3'\n______________CGGAGAAA_GCAG___GC\n______________\|::\|\|\|\|\|_\|\|\|\|___\|\|\n______________GUUUCUUU_CGUC___CG\n3'-UUU...CUGUA________U____AC___-5'\n_____________\|_________________\|\n_____________18________________1\n	179 -- 185	10 -- 16	-17.1669 kcal/mol	3.03232 kcal/mol	1.43853 kcal/mol	177 196@LB@ \| \|@LB@5'-GCC...CAUGC U GAA ACGCU...AGA-3'@LB@ CGGAGAAA GCAG GC@LB@ \|::\|\|\|\|\| \|\|\|\| \|\|@LB@ GUUUCUUU CGUC CG@LB@3'-UUU...CUGUA U AC -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -17.1669 kcal/mol@LB@Unfolding Energy - mRNA 3.03232 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 10 -- 16@LB@
112	0.007494	0.2348	b2529	iscU	-11.51	0.152972	152 -- 183	2 -- 33	iron-sulfur cluster assembly scaffold protein		_____________151______________________________184\n_____________\|________________________________\|\n5'-UGG...AACAG___C_______CU_____UUAAUC____UC__AAUCA...GGG-3'\n______________CAU_GAAUGGG__CAUCA______GGUA__GG\n______________\|\|:_:\|\|\|\|\|\|__\|\|\|\|\|______:\|:\|__\|\|\n______________GUG_UUUACCC__GUAGU______UCGU__CC\n3'-UUU...CCGAG___U_______CU_____UUCUUU____CA__G-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	156 -- 162	23 -- 29	-21.7 kcal/mol	7.11537 kcal/mol	3.07861 kcal/mol	151 184@LB@ \| \|@LB@5'-UGG...AACAG C CU UUAAUC UC AAUCA...GGG-3'@LB@ CAU GAAUGGG CAUCA GGUA GG@LB@ \|\|: :\|\|\|\|\|\| \|\|\|\|\| :\|:\| \|\|@LB@ GUG UUUACCC GUAGU UCGU CC@LB@3'-UUU...CCGAG U CU UUCUUU CA G-5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -21.7 kcal/mol@LB@Unfolding Energy - mRNA 7.11537 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 152 -- 183@LB@Position - sRNA 2 -- 33@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 23 -- 29@LB@
126	0.009112	0.2491	b0299	insF1	-12.99	0.078544	136 -- 158	1 -- 32	IS3 transposase B	b0372 b0541 b1026 b2089 b3558	_____________135______________________________159\n_____________\|________________________________\|\n5'-ACU...AGCUG______C_________________________UAUCC...GUC-3'\n______________GCAGAA__GGGAU______GAAGAGC__UGGC\n______________:\|\|:\|\|__\|\|\|\|:______\|\|\|:\|\|\|__\|\|\|\|\n______________UGUUUU__CCCUG______CUUUUCG__ACCG\n3'-UUU...CGAGG______AC_____UAGUUU_______UC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	148 -- 154	7 -- 13	-22.7833 kcal/mol	7.25293 kcal/mol	2.53929 kcal/mol	135 159@LB@ \| \|@LB@5'-ACU...AGCUG C UAUCC...GUC-3'@LB@ GCAGAA GGGAU GAAGAGC UGGC@LB@ :\|\|:\|\| \|\|\|\|: \|\|\|:\|\|\| \|\|\|\|@LB@ UGUUUU CCCUG CUUUUCG ACCG@LB@3'-UUU...CGAGG AC UAGUUU UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.99 kcal/mol@LB@Hybridization Energy -22.7833 kcal/mol@LB@Unfolding Energy - mRNA 7.25293 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 136 -- 158@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 7 -- 13@LB@
61	0.00311	0.1789	b0224	yafK	-14.83	0.030578	183 -- 204	1 -- 20	L D-transpeptidase-related protein		_____________182____________________205\n_____________\|______________________\|\n5'-UUA...CGUUU__________U_______AU__GUAAA...AAG-3'\n______________UAUCAAGGAA_AAGCAGU__GC\n______________:\|\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________GUAGUUUCUU_UUCGUCA__CG\n3'-UUU...CCCCU__________________C___-5'\n_____________\|_____________________\|\n_____________21____________________1\n	194 -- 200	4 -- 10	-21.3079 kcal/mol	5.02402 kcal/mol	1.45855 kcal/mol	182 205@LB@ \| \|@LB@5'-UUA...CGUUU U AU GUAAA...AAG-3'@LB@ UAUCAAGGAA AAGCAGU GC@LB@ :\|\|\|\|\|:\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GUAGUUUCUU UUCGUCA CG@LB@3'-UUU...CCCCU C -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -14.83 kcal/mol@LB@Hybridization Energy -21.3079 kcal/mol@LB@Unfolding Energy - mRNA 5.02402 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 183 -- 204@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 4 -- 10@LB@
181	0.01309	0.2504	b2799	fucO	-15.36	0.022654	183 -- 205	1 -- 21	L-1 2-propanediol oxidoreductase		_____________182_____________________206\n_____________\|_______________________\|\n5'-CUU...GUAAA___A__________G_U_A____UAACA...CGC-3'\n______________GCA_CAAGGAGAAG_A_G_UGGC\n______________:\|\|_\|\|\|:\|\|:\|\|\|_\|_\|_\|\|\|\|\n______________UGU_GUUUCUUUUC_U_C_ACCG\n3'-UUU...ACCCC___A__________G________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	190 -- 196	8 -- 14	-20.3858 kcal/mol	3.51699 kcal/mol	1.51103 kcal/mol	182 206@LB@ \| \|@LB@5'-CUU...GUAAA A G U A UAACA...CGC-3'@LB@ GCA CAAGGAGAAG A G UGGC@LB@ :\|\| \|\|\|:\|\|:\|\|\| \| \| \|\|\|\|@LB@ UGU GUUUCUUUUC U C ACCG@LB@3'-UUU...ACCCC A G -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -20.3858 kcal/mol@LB@Unfolding Energy - mRNA 3.51699 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 8 -- 14@LB@
196	0.01416	0.2529	b0870	ltaE	-12.27	0.109556	23 -- 39	7 -- 23	L-allo-threonine aldolase PLP-dependent		_____________22________________40\n_____________\|_________________\|\n5'-GUC...GUGGU__U__C___________UAGCC...ACC-3'\n______________GG_CG_CAAAGAAGAGU\n______________\|\|_\|:_\|\|\|\|\|\|\|:\|\|:\n______________CC_GU_GUUUCUUUUCG\n3'-UUU...UUACC__U__A___________UCACCG-5'\n_____________\|_________________\|\n_____________24________________6\n	33 -- 39	7 -- 13	-15.8177 kcal/mol	2.94498 kcal/mol	0.599063 kcal/mol	22 40@LB@ \| \|@LB@5'-GUC...GUGGU U C UAGCC...ACC-3'@LB@ GG CG CAAAGAAGAGU@LB@ \|\| \|: \|\|\|\|\|\|\|:\|\|:@LB@ CC GU GUUUCUUUUCG@LB@3'-UUU...UUACC U A UCACCG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -15.8177 kcal/mol@LB@Unfolding Energy - mRNA 2.94498 kcal/mol@LB@Unfolding Energy - sRNA 0.599063 kcal/mol@LB@@LB@Position - mRNA 23 -- 39@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 7 -- 13@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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