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
111	0.007434	0.2348	b0103	coaE	-19.66	0.001155	224 -- 242	1 -- 25	dephospho-CoA kinase		_____________223________________________243\n_____________\|__________________________\|\n5'-UAU...UUAAC___A______________________AAGAG...AUA-3'\n______________GGG_GGCAUU_______GGCAGUGGC\n______________\|\|\|_\|:\|\|\|:_______:\|\|\|\|\|\|\|\|\n______________CCC_CUGUAG_______UCGUCACCG\n3'-UUU...UUUUA__________UUUCUUU_________-5'\n_____________\|_________________________\|\n_____________26________________________1\n	236 -- 242	1 -- 7	-28.3462 kcal/mol	6.16994 kcal/mol	2.51748 kcal/mol	223 243@LB@ \| \|@LB@5'-UAU...UUAAC A AAGAG...AUA-3'@LB@ GGG GGCAUU GGCAGUGGC@LB@ \|\|\| \|:\|\|\|: :\|\|\|\|\|\|\|\|@LB@ CCC CUGUAG UCGUCACCG@LB@3'-UUU...UUUUA UUUCUUU -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -19.66 kcal/mol@LB@Hybridization Energy -28.3462 kcal/mol@LB@Unfolding Energy - mRNA 6.16994 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 224 -- 242@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 1 -- 7@LB@
81	0.004938	0.2139	b0115	aceF	-13.95	0.048783	266 -- 289	7 -- 31	pyruvate dehydrogenase dihydrolipoyltransacetylase component E2		_____________265_________________________290\n_____________\|___________________________\|\n5'-GAU...CUGGU_________C__________UU_____CGAAC...CGC-3'\n______________CAAAGUGGG_GACA___AAG__GAAGC\n______________\|\|\|\|:\|\|\|\|_\|\|\|\|___\|\|\|__:\|\|\|\|\n______________GUUUUACCC_CUGU___UUC__UUUCG\n3'-UUU...GAGGU______________AGU___U______UCACCG-5'\n_____________\|___________________________\|\n_____________32__________________________6\n	268 -- 274	23 -- 29	-21.1287 kcal/mol	4.65658 kcal/mol	2.52208 kcal/mol	265 290@LB@ \| \|@LB@5'-GAU...CUGGU C UU CGAAC...CGC-3'@LB@ CAAAGUGGG GACA AAG GAAGC@LB@ \|\|\|\|:\|\|\|\| \|\|\|\| \|\|\| :\|\|\|\|@LB@ GUUUUACCC CUGU UUC UUUCG@LB@3'-UUU...GAGGU AGU U UCACCG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -21.1287 kcal/mol@LB@Unfolding Energy - mRNA 4.65658 kcal/mol@LB@Unfolding Energy - sRNA 2.52208 kcal/mol@LB@@LB@Position - mRNA 266 -- 289@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 23 -- 29@LB@
119	0.008338	0.2459	b0123	cueO	-14.31	0.040489	47 -- 61	9 -- 24	multicopper oxidase (laccase)		_____________46_______________62\n_____________\|________________\|\n5'-CUG...UACCA________________UAAAC...CGU-3'\n______________GGGGC_UUAAAGAAGA\n______________\|\|\|:\|_\|:\|\|\|\|\|\|:\|\n______________CCCUG_AGUUUCUUUU\n3'-UUU...UUUAC_____U__________CGUCACCG-5'\n_____________\|________________\|\n_____________25_______________8\n	55 -- 61	9 -- 15	-17.0719 kcal/mol	2.10565 kcal/mol	0.659805 kcal/mol	46 62@LB@ \| \|@LB@5'-CUG...UACCA UAAAC...CGU-3'@LB@ GGGGC UUAAAGAAGA@LB@ \|\|\|:\| \|:\|\|\|\|\|\|:\|@LB@ CCCUG AGUUUCUUUU@LB@3'-UUU...UUUAC U CGUCACCG-5'@LB@ \| \|@LB@ 25 8@LB@@LB@@LB@Energy -14.31 kcal/mol@LB@Hybridization Energy -17.0719 kcal/mol@LB@Unfolding Energy - mRNA 2.10565 kcal/mol@LB@Unfolding Energy - sRNA 0.659805 kcal/mol@LB@@LB@Position - mRNA 47 -- 61@LB@Position - sRNA 9 -- 24@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 9 -- 15@LB@
124	0.008958	0.2491	b0124	gcd	-13.85	0.051383	179 -- 193	48 -- 62	glucose dehydrogenase		_____________178_____________194\n_____________\|_______________\|\n5'-UAA...AUUAA_______________UCUCU...GGC-3'\n______________UGAAUUGAAAUGGUG\n______________\|\|\|\|::\|\|\|\|\|\|\|:\|\n______________ACUUGGCUUUACCGC\n3'-UUU...UUGGA_______________CCCAA...CCG-5'\n_____________\|_______________\|\n_____________63______________47\n	187 -- 193	48 -- 54	-20.4838 kcal/mol	2.67361 kcal/mol	3.96136 kcal/mol	178 194@LB@ \| \|@LB@5'-UAA...AUUAA UCUCU...GGC-3'@LB@ UGAAUUGAAAUGGUG@LB@ \|\|\|\|::\|\|\|\|\|\|\|:\|@LB@ ACUUGGCUUUACCGC@LB@3'-UUU...UUGGA CCCAA...CCG-5'@LB@ \| \|@LB@ 63 47@LB@@LB@@LB@Energy -13.85 kcal/mol@LB@Hybridization Energy -20.4838 kcal/mol@LB@Unfolding Energy - mRNA 2.67361 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 179 -- 193@LB@Position - sRNA 48 -- 62@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 48 -- 54@LB@
54	0.00267	0.1735	b0131	panD	-12.96	0.079905	178 -- 195	5 -- 22	aspartate 1-decarboxylase		_____________177________________196\n_____________\|__________________\|\n5'-AUU...UUAAC____GGGU__________AAGUU...UUG-3'\n______________GACA____AGAAAGGUAG\n______________\|\|\|\|____\|\|\|\|\|:\|:\|\|\n______________CUGU____UCUUUUCGUC\n3'-UUU...UACCC____AGUU__________ACCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	189 -- 195	5 -- 11	-16.4376 kcal/mol	1.9462 kcal/mol	1.53637 kcal/mol	177 196@LB@ \| \|@LB@5'-AUU...UUAAC GGGU AAGUU...UUG-3'@LB@ GACA AGAAAGGUAG@LB@ \|\|\|\| \|\|\|\|\|:\|:\|\|@LB@ CUGU UCUUUUCGUC@LB@3'-UUU...UACCC AGUU ACCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -12.96 kcal/mol@LB@Hybridization Energy -16.4376 kcal/mol@LB@Unfolding Energy - mRNA 1.9462 kcal/mol@LB@Unfolding Energy - sRNA 1.53637 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 5 -- 11@LB@
15	0.0006403	0.1243	b0178	skp	-17.37	0.006465	90 -- 106	1 -- 17	periplasmic chaperone		_____________89________________107\n_____________\|_________________\|\n5'-CUC...CUCCA________U________AGUGU...UCC-3'\n______________CAAAGGAA_GUAGUGGU\n______________\|\|\|\|\|:\|\|_\|:\|\|\|\|\|:\n______________GUUUCUUU_CGUCACCG\n3'-UUU...CUGUA________U________-5'\n_____________\|________________\|\n_____________18_______________1\n	100 -- 106	1 -- 7	-21.6829 kcal/mol	2.87621 kcal/mol	1.43853 kcal/mol	89 107@LB@ \| \|@LB@5'-CUC...CUCCA U AGUGU...UCC-3'@LB@ CAAAGGAA GUAGUGGU@LB@ \|\|\|\|\|:\|\| \|:\|\|\|\|\|:@LB@ GUUUCUUU CGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -17.37 kcal/mol@LB@Hybridization Energy -21.6829 kcal/mol@LB@Unfolding Energy - mRNA 2.87621 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 90 -- 106@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 1 -- 7@LB@
156	0.01139	0.2504	b0197	metQ	-9.46	0.330846	169 -- 205	1 -- 33	DL-methionine transporter subunit		_____________168_____________________________________206\n_____________\|_______________________________________\|\n5'-GUG...UUCAA_____CAUAAAUA___________GAAUAA_________GUUCA...UUA-3'\n______________CACAA_________AUUGAAGAAG______GGUA_UGGC\n______________\|\|\|\|\|_________\|\|::\|\|\|\|\|:______:\|:\|_\|\|\|\|\n______________GUGUU_________UAGUUUCUUU______UCGU_ACCG\n3'-UUU...CCGAG_____UUACCCCUG____________________C____-5'\n_____________\|______________________________________\|\n_____________34_____________________________________1\n	185 -- 191	10 -- 16	-16.9822 kcal/mol	4.44131 kcal/mol	3.07861 kcal/mol	168 206@LB@ \| \|@LB@5'-GUG...UUCAA CAUAAAUA GAAUAA GUUCA...UUA-3'@LB@ CACAA AUUGAAGAAG GGUA UGGC@LB@ \|\|\|\|\| \|\|::\|\|\|\|\|: :\|:\| \|\|\|\|@LB@ GUGUU UAGUUUCUUU UCGU ACCG@LB@3'-UUU...CCGAG UUACCCCUG C -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -16.9822 kcal/mol@LB@Unfolding Energy - mRNA 4.44131 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 169 -- 205@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 10 -- 16@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@
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@
200	0.01506	0.259	b0404	acpH	-14.03	0.046767	57 -- 80	6 -- 28	acyl carrier protein (ACP) phosphodiesterase; ACP hydrolyase		_____________56________________________81\n_____________\|_________________________\|\n5'-GCC...GGGAU______CA_________UUC_____AUUCA...GUU-3'\n______________AGUGGG___AUCAGGGA___GGGCA\n______________\|:\|\|\|\|___\|\|\|\|::\|\|___::\|\|\|\n______________UUACCC___UAGUUUCU___UUCGU\n3'-UUU...GUGUU______CUG________U_______CACCG-5'\n_____________\|_________________________\|\n_____________29________________________5\n	66 -- 72	12 -- 18	-19.5231 kcal/mol	4.78501 kcal/mol	0.706454 kcal/mol	56 81@LB@ \| \|@LB@5'-GCC...GGGAU CA UUC AUUCA...GUU-3'@LB@ AGUGGG AUCAGGGA GGGCA@LB@ \|:\|\|\|\| \|\|\|\|::\|\| ::\|\|\|@LB@ UUACCC UAGUUUCU UUCGU@LB@3'-UUU...GUGUU CUG U CACCG-5'@LB@ \| \|@LB@ 29 5@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -19.5231 kcal/mol@LB@Unfolding Energy - mRNA 4.78501 kcal/mol@LB@Unfolding Energy - sRNA 0.706454 kcal/mol@LB@@LB@Position - mRNA 57 -- 80@LB@Position - sRNA 6 -- 28@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 12 -- 18@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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