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
111	0.009564	0.2693	b2040	rfbD	-5.00	0.321114	87 -- 99	24 -- 42	dTDP-L-rhamnose synthase NAD(P)-dependent dTDP-4-dehydrorhamnose reductase subunit	_____________86__________________100\n_____________\|___________________\|\n5'-GAU...UUUGA___________________AAAAC...CUA-3'\n______________GAGCG______GGAUUCGU\n______________:\|\|\|:______::\|\|\|\|\|\|\n______________UUCGU______UUUAAGCA\n3'-UUU...CGUUC_____GAAUUU________AUGUG...CAA-5'\n_____________\|___________________\|\n_____________43__________________23\n	93 -- 99	24 -- 30	-9.51502 kcal/mol	2.86783 kcal/mol	1.64896 kcal/mol	86 100@LB@ \| \|@LB@5'-GAU...UUUGA AAAAC...CUA-3'@LB@ GAGCG GGAUUCGU@LB@ :\|\|\|: ::\|\|\|\|\|\|@LB@ UUCGU UUUAAGCA@LB@3'-UUU...CGUUC GAAUUU AUGUG...CAA-5'@LB@ \| \|@LB@ 43 23@LB@@LB@@LB@Energy -5.00 kcal/mol@LB@Hybridization Energy -9.51502 kcal/mol@LB@Unfolding Energy - mRNA 2.86783 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 87 -- 99@LB@Position - sRNA 24 -- 42@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 24 -- 30@LB@
78	0.004685	0.1935	b3905	rhaS	-7.96	0.061746	70 -- 86	26 -- 40	transcriptional activator of rhaBAD and rhaT	_____________69________________87\n_____________\|_________________\|\n5'-UGG...UCACC______CCU________ACGCU...AUG-3'\n______________GCAUUU___GAAAAUUC\n______________\|\|\|:\|\|___:\|\|\|\|\|\|\|\n______________CGUGAA___UUUUUAAG\n3'-UUU...UUCUU______U__________CAAUG...CAA-5'\n_____________\|_________________\|\n_____________41________________25\n	80 -- 86	26 -- 32	-11.6625 kcal/mol	2.05222 kcal/mol	1.64811 kcal/mol	69 87@LB@ \| \|@LB@5'-UGG...UCACC CCU ACGCU...AUG-3'@LB@ GCAUUU GAAAAUUC@LB@ \|\|\|:\|\| :\|\|\|\|\|\|\|@LB@ CGUGAA UUUUUAAG@LB@3'-UUU...UUCUU U CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -11.6625 kcal/mol@LB@Unfolding Energy - mRNA 2.05222 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 70 -- 86@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 26 -- 32@LB@
23	0.000685	0.09021	b3780	rhlB	-7.99	0.060609	254 -- 278	29 -- 60	ATP-dependent RNA helicase	_____________253______________________________279\n_____________\|________________________________\|\n5'-UCG...CAUCC____G_________________C_________AAAGG...CGC-3'\n______________GAAG_UUGU_______AGAAGC_CUUGAAAAA\n______________\|\|\|:_\|\|\|:_______\|\|\|\|\|\|_\|\|\|:\|\|\|\|\|\n______________CUUU_AACG_______UCUUCG_GAAUUUUUU\n3'-UUU...CCCUA____G____AAUUCGU______U_________AAGCA...CAA-5'\n_____________\|________________________________\|\n_____________61_______________________________28\n	270 -- 276	31 -- 37	-19.7636 kcal/mol	5.50064 kcal/mol	6.27092 kcal/mol	253 279@LB@ \| \|@LB@5'-UCG...CAUCC G C AAAGG...CGC-3'@LB@ GAAG UUGU AGAAGC CUUGAAAAA@LB@ \|\|\|: \|\|\|: \|\|\|\|\|\| \|\|\|:\|\|\|\|\|@LB@ CUUU AACG UCUUCG GAAUUUUUU@LB@3'-UUU...CCCUA G AAUUCGU U AAGCA...CAA-5'@LB@ \| \|@LB@ 61 28@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -19.7636 kcal/mol@LB@Unfolding Energy - mRNA 5.50064 kcal/mol@LB@Unfolding Energy - sRNA 6.27092 kcal/mol@LB@@LB@Position - mRNA 254 -- 278@LB@Position - sRNA 29 -- 60@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 31 -- 37@LB@
175	0.01993	0.3669	b0183	rnhB	-5.94	0.199165	195 -- 215	23 -- 41	ribonuclease HII degrades RNA of DNA-RNA hybrids	_____________194___________________216\n_____________\|_____________________\|\n5'-AAU...GAGUU_____AA___UC_________UAUCC...UCC-3'\n______________AGCAC__UGA__GAAUUUGUU\n______________\|\|\|\|\|__\|:\|__:\|\|\|\|:\|\|\|\n______________UCGUG__AUU__UUUAAGCAA\n3'-UUU...GUUCU_____A____U__________UGUGG...CAA-5'\n_____________\|_____________________\|\n_____________42____________________22\n	209 -- 215	23 -- 29	-11.3649 kcal/mol	3.77136 kcal/mol	1.64896 kcal/mol	194 216@LB@ \| \|@LB@5'-AAU...GAGUU AA UC UAUCC...UCC-3'@LB@ AGCAC UGA GAAUUUGUU@LB@ \|\|\|\|\| \|:\| :\|\|\|\|:\|\|\|@LB@ UCGUG AUU UUUAAGCAA@LB@3'-UUU...GUUCU A U UGUGG...CAA-5'@LB@ \| \|@LB@ 42 22@LB@@LB@@LB@Energy -5.94 kcal/mol@LB@Hybridization Energy -11.3649 kcal/mol@LB@Unfolding Energy - mRNA 3.77136 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 195 -- 215@LB@Position - sRNA 23 -- 41@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 23 -- 29@LB@
132	0.01257	0.3067	b2516	rodZ	-8.98	0.032240	231 -- 240	34 -- 43	MreB assembly cytoskeletal protein	_____________230________241\n_____________\|__________\|\n5'-UAA...AAAAU__________CUACC...UUG-3'\n______________GAAGCACUUA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CUUCGUGAAU\n3'-UUU...UCGUU__________UUUUU...CAA-5'\n_____________\|__________\|\n_____________44_________33\n	234 -- 240	34 -- 40	-13.7965 kcal/mol	1.10051 kcal/mol	3.71643 kcal/mol	230 241@LB@ \| \|@LB@5'-UAA...AAAAU CUACC...UUG-3'@LB@ GAAGCACUUA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CUUCGUGAAU@LB@3'-UUU...UCGUU UUUUU...CAA-5'@LB@ \| \|@LB@ 44 33@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -13.7965 kcal/mol@LB@Unfolding Energy - mRNA 1.10051 kcal/mol@LB@Unfolding Energy - sRNA 3.71643 kcal/mol@LB@@LB@Position - mRNA 231 -- 240@LB@Position - sRNA 34 -- 43@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 34 -- 40@LB@
123	0.0108	0.2828	b2606	rplS	-6.81	0.122900	220 -- 252	37 -- 58	50S ribosomal subunit protein L19	_____________219_______________________________253\n_____________\|_________________________________\|\n5'-AUA...UAAGC______AACAAGAGCAGAUG________C____CUUCC...UUG-3'\n______________AACUUG______________AAGCAGGA_GUAC\n______________\|\|\|\|\|\|______________\|\|\|\|\|:\|\|_\|:\|\|\n______________UUGAAC______________UUCGUUCU_CGUG\n3'-UUU...CUACU______GAA___________________U____AAUUU...CAA-5'\n_____________\|_________________________________\|\n_____________59________________________________36\n	241 -- 247	42 -- 48	-17.5998 kcal/mol	4.54246 kcal/mol	6.24354 kcal/mol	219 253@LB@ \| \|@LB@5'-AUA...UAAGC AACAAGAGCAGAUG C CUUCC...UUG-3'@LB@ AACUUG AAGCAGGA GUAC@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|\| \|:\|\|@LB@ UUGAAC UUCGUUCU CGUG@LB@3'-UUU...CUACU GAA U AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -17.5998 kcal/mol@LB@Unfolding Energy - mRNA 4.54246 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 220 -- 252@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 42 -- 48@LB@
191	0.02253	0.38	b3186	rplU	-5.10	0.305418	95 -- 102	34 -- 41	50S ribosomal subunit protein L21	_____________94_______103\n_____________\|________\|\n5'-UUA...ACUGU________UCAAA...UUG-3'\n______________AGCACUUG\n______________\|\|\|\|\|\|\|:\n______________UCGUGAAU\n3'-UUU...GUUCU________UUUUU...CAA-5'\n_____________\|________\|\n_____________42_______33\n	96 -- 102	34 -- 40	-9.60207 kcal/mol	2.88333 kcal/mol	1.6155 kcal/mol	94 103@LB@ \| \|@LB@5'-UUA...ACUGU UCAAA...UUG-3'@LB@ AGCACUUG@LB@ \|\|\|\|\|\|\|:@LB@ UCGUGAAU@LB@3'-UUU...GUUCU UUUUU...CAA-5'@LB@ \| \|@LB@ 42 33@LB@@LB@@LB@Energy -5.10 kcal/mol@LB@Hybridization Energy -9.60207 kcal/mol@LB@Unfolding Energy - mRNA 2.88333 kcal/mol@LB@Unfolding Energy - sRNA 1.6155 kcal/mol@LB@@LB@Position - mRNA 95 -- 102@LB@Position - sRNA 34 -- 41@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 34 -- 40@LB@
38	0.00143	0.1212	b3315	rplV	-7.95	0.062235	2 -- 19	23 -- 40	50S ribosomal subunit protein L22	_____________1__________________20\n_____________\|__________________\|\n__________5'-C________UCCCG_____CAACG...UGG-3'\n______________GCACUUGG_____UCGUU\n______________\|\|\|\|\|\|::_____\|\|\|\|\|\n______________CGUGAAUU_____AGCAA\n3'-UUU...UUCUU________UUUUA_____UGUGG...CAA-5'\n_____________\|__________________\|\n_____________41_________________22\n	3 -- 9	33 -- 39	-14.4443 kcal/mol	4.84591 kcal/mol	1.64885 kcal/mol	1 20@LB@ \| \|@LB@ 5'-C UCCCG CAACG...UGG-3'@LB@ GCACUUGG UCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|@LB@ CGUGAAUU AGCAA@LB@3'-UUU...UUCUU UUUUA UGUGG...CAA-5'@LB@ \| \|@LB@ 41 22@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -14.4443 kcal/mol@LB@Unfolding Energy - mRNA 4.84591 kcal/mol@LB@Unfolding Energy - sRNA 1.64885 kcal/mol@LB@@LB@Position - mRNA 2 -- 19@LB@Position - sRNA 23 -- 40@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 33 -- 39@LB@
128	0.01225	0.3033	b3299	rpmJ	-5.94	0.199813	193 -- 212	24 -- 42	50S ribosomal subunit protein L36	_____________192__________________213\n_____________\|____________________\|\n5'-GGA...ACGGA_____AAAAU__________GCUUC...AUA-3'\n______________GAGUA_____GAAAGUUCGU\n______________:\|\|:\|_____:\|\|\|:\|\|\|\|\|\n______________UUCGU_____UUUUUAAGCA\n3'-UUU...CGUUC_____GAAU___________AUGUG...CAA-5'\n_____________\|____________________\|\n_____________43___________________23\n	206 -- 212	24 -- 30	-12.4383 kcal/mol	4.85088 kcal/mol	1.64896 kcal/mol	192 213@LB@ \| \|@LB@5'-GGA...ACGGA AAAAU GCUUC...AUA-3'@LB@ GAGUA GAAAGUUCGU@LB@ :\|\|:\| :\|\|\|:\|\|\|\|\|@LB@ UUCGU UUUUUAAGCA@LB@3'-UUU...CGUUC GAAU AUGUG...CAA-5'@LB@ \| \|@LB@ 43 23@LB@@LB@@LB@Energy -5.94 kcal/mol@LB@Hybridization Energy -12.4383 kcal/mol@LB@Unfolding Energy - mRNA 4.85088 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 193 -- 212@LB@Position - sRNA 24 -- 42@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 24 -- 30@LB@
36	0.001384	0.121	b2573	rpoE	-5.96	0.197133	163 -- 178	25 -- 41	RNA polymerase sigma E factor	_____________162_______________179\n_____________\|_________________\|\n5'-ACA...UCGAU_____GU__________GUUUG...UGG-3'\n______________AGCGC___GGAAAUUUG\n______________\|\|\|:\|___::\|\|\|\|\|:\|\n______________UCGUG___UUUUUAAGC\n3'-UUU...GUUCU_____AAU_________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	172 -- 178	25 -- 31	-12.5895 kcal/mol	4.97735 kcal/mol	1.64839 kcal/mol	162 179@LB@ \| \|@LB@5'-ACA...UCGAU GU GUUUG...UGG-3'@LB@ AGCGC GGAAAUUUG@LB@ \|\|\|:\| ::\|\|\|\|\|:\|@LB@ UCGUG UUUUUAAGC@LB@3'-UUU...GUUCU AAU AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -5.96 kcal/mol@LB@Hybridization Energy -12.5895 kcal/mol@LB@Unfolding Energy - mRNA 4.97735 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 163 -- 178@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 25 -- 31@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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