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
18	0.0007186	0.1243	b3657	yicJ	-19.60	0.001218	184 -- 200	5 -- 21	putative transporter		_____________183_______________201\n_____________\|_________________\|\n5'-CAG...CUAUA_________________AUGAA...UGU-3'\n______________GCAUCAAGGAAAAGCAG\n______________:\|\|\|\|\|\|:\|\|\|\|\|\|\|\|\|\n______________UGUAGUUUCUUUUCGUC\n3'-UUU...ACCCC_________________ACCG-5'\n_____________\|_________________\|\n_____________22________________4\n	194 -- 200	5 -- 11	-25.6417 kcal/mol	4.53845 kcal/mol	1.5073 kcal/mol	183 201@LB@ \| \|@LB@5'-CAG...CUAUA AUGAA...UGU-3'@LB@ GCAUCAAGGAAAAGCAG@LB@ :\|\|\|\|\|\|:\|\|\|\|\|\|\|\|\|@LB@ UGUAGUUUCUUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -19.60 kcal/mol@LB@Hybridization Energy -25.6417 kcal/mol@LB@Unfolding Energy - mRNA 4.53845 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 184 -- 200@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
24	0.0009771	0.1361	b4295	yjhU	-16.20	0.013710	198 -- 226	5 -- 30	putative DNA-binding transcriptional regulator; KpLE2 phage-like element	b1512	_____________197___________________________227\n_____________\|_____________________________\|\n5'-GUA...AUACA_______AUA__G______C___C_____CCUGU...UUG-3'\n______________AAAGUGG___GA_AUCAAA_AAA_AGCAG\n______________\|\|\|:\|\|\|___\|\|_\|\|\|\|\|\|_\|\|\|_\|\|\|\|\|\n______________UUUUACC___CU_UAGUUU_UUU_UCGUC\n3'-UUU...AGGUG_______C____G______C_________ACCG-5'\n_____________\|_____________________________\|\n_____________31____________________________4\n	198 -- 204	24 -- 30	-21.4023 kcal/mol	2.69702 kcal/mol	2.50278 kcal/mol	197 227@LB@ \| \|@LB@5'-GUA...AUACA AUA G C C CCUGU...UUG-3'@LB@ AAAGUGG GA AUCAAA AAA AGCAG@LB@ \|\|\|:\|\|\| \|\| \|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ UUUUACC CU UAGUUU UUU UCGUC@LB@3'-UUU...AGGUG C G C ACCG-5'@LB@ \| \|@LB@ 31 4@LB@@LB@@LB@Energy -16.20 kcal/mol@LB@Hybridization Energy -21.4023 kcal/mol@LB@Unfolding Energy - mRNA 2.69702 kcal/mol@LB@Unfolding Energy - sRNA 2.50278 kcal/mol@LB@@LB@Position - mRNA 198 -- 226@LB@Position - sRNA 5 -- 30@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 24 -- 30@LB@
42	0.002133	0.1648	b0968	yccX	-12.44	0.101807	184 -- 198	5 -- 23	weak acylphosphatase		_____________183_________________199\n_____________\|___________________\|\n5'-GGC...AUUAA___________________CAAUG...CCG-3'\n______________GGAUA____AGGAGAGCAG\n______________\|\|\|:\|____\|\|:\|:\|\|\|\|\|\n______________CCUGU____UCUUUUCGUC\n3'-UUU...UUACC_____AGUU__________ACCG-5'\n_____________\|___________________\|\n_____________24__________________4\n	192 -- 198	5 -- 11	-17.1825 kcal/mol	3.17176 kcal/mol	1.57523 kcal/mol	183 199@LB@ \| \|@LB@5'-GGC...AUUAA CAAUG...CCG-3'@LB@ GGAUA AGGAGAGCAG@LB@ \|\|\|:\| \|\|:\|:\|\|\|\|\|@LB@ CCUGU UCUUUUCGUC@LB@3'-UUU...UUACC AGUU ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -17.1825 kcal/mol@LB@Unfolding Energy - mRNA 3.17176 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 184 -- 198@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@LB@
44	0.002166	0.1648	b3349	slyD	-19.18	0.001707	20 -- 41	5 -- 23	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)		_____________19_____________________42\n_____________\|______________________\|\n5'-UGU...AGUGC__________UGC_________ACAAA...ACU-3'\n______________GGACAUCAGA___GAGAAGCAG\n______________\|\|\|\|\|\|\|\|:\|___\|\|:\|\|\|\|\|\|\n______________CCUGUAGUUU___CUUUUCGUC\n3'-UUU...UUACC______________________ACCG-5'\n_____________\|______________________\|\n_____________24_____________________4\n	35 -- 41	5 -- 11	-25.7728 kcal/mol	5.01574 kcal/mol	1.57523 kcal/mol	19 42@LB@ \| \|@LB@5'-UGU...AGUGC UGC ACAAA...ACU-3'@LB@ GGACAUCAGA GAGAAGCAG@LB@ \|\|\|\|\|\|\|\|:\| \|\|:\|\|\|\|\|\|@LB@ CCUGUAGUUU CUUUUCGUC@LB@3'-UUU...UUACC ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -19.18 kcal/mol@LB@Hybridization Energy -25.7728 kcal/mol@LB@Unfolding Energy - mRNA 5.01574 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 20 -- 41@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 5 -- 11@LB@
52	0.002562	0.1729	b0881	clpS	-16.21	0.013666	11 -- 25	5 -- 25	regulatory protein for ClpA substrate specificity		_____________10____________________26\n_____________\|_____________________\|\n5'-GCA...UGACA_____________________GUAUG...UCA-3'\n______________GGGGACA______AGGGGCAG\n______________\|\|\|\|\|\|\|______\|:::\|\|\|\|\n______________CCCCUGU______UUUUCGUC\n3'-UUU...UUUUA_______AGUUUC________ACCG-5'\n_____________\|_____________________\|\n_____________26____________________4\n	19 -- 25	5 -- 11	-21.27 kcal/mol	2.56205 kcal/mol	2.50017 kcal/mol	10 26@LB@ \| \|@LB@5'-GCA...UGACA GUAUG...UCA-3'@LB@ GGGGACA AGGGGCAG@LB@ \|\|\|\|\|\|\| \|:::\|\|\|\|@LB@ CCCCUGU UUUUCGUC@LB@3'-UUU...UUUUA AGUUUC ACCG-5'@LB@ \| \|@LB@ 26 4@LB@@LB@@LB@Energy -16.21 kcal/mol@LB@Hybridization Energy -21.27 kcal/mol@LB@Unfolding Energy - mRNA 2.56205 kcal/mol@LB@Unfolding Energy - sRNA 2.50017 kcal/mol@LB@@LB@Position - mRNA 11 -- 25@LB@Position - sRNA 5 -- 25@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 5 -- 11@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@
68	0.003723	0.191	b3131	agaR	-11.10	0.180958	280 -- 299	5 -- 22	transcriptional repressor of the aga regulon		_____________279__________________300\n_____________\|____________________\|\n5'-CAG...UCUGC____G________UGU____G-3'\n______________GACA_CAAGGGAG___GCAG\n______________\|\|\|\|_\|\|\|:\|:\|:___\|\|\|\|\n______________CUGU_GUUUCUUU___CGUC\n3'-UUU...UACCC____A________U______ACCG-5'\n_____________\|____________________\|\n_____________23___________________4\n	286 -- 292	10 -- 16	-17.5345 kcal/mol	4.90034 kcal/mol	1.53637 kcal/mol	279 300@LB@ \| \|@LB@5'-CAG...UCUGC G UGU G-3'@LB@ GACA CAAGGGAG GCAG@LB@ \|\|\|\| \|\|\|:\|:\|: \|\|\|\|@LB@ CUGU GUUUCUUU CGUC@LB@3'-UUU...UACCC A U ACCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -17.5345 kcal/mol@LB@Unfolding Energy - mRNA 4.90034 kcal/mol@LB@Unfolding Energy - sRNA 1.53637 kcal/mol@LB@@LB@Position - mRNA 280 -- 299@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 10 -- 16@LB@
88	0.005527	0.2147	b3525	yhjH	-13.65	0.056862	190 -- 212	5 -- 23	cyclic-di-GMP phosphodiesterase FlhDC-regulated		_____________189_____________________213\n_____________\|_______________________\|\n5'-UUA...ACACA_______UUU__UGAU_______GUUAU...CCU-3'\n______________GGACAUC___GA____AAGGCAG\n______________\|\|\|\|\|\|\|___\|\|____\|\|:\|\|\|\|\n______________CCUGUAG___CU____UUUCGUC\n3'-UUU...UUACC_______UUU_____________ACCG-5'\n_____________\|_______________________\|\n_____________24______________________4\n	206 -- 212	5 -- 11	-19.0549 kcal/mol	3.83037 kcal/mol	1.57523 kcal/mol	189 213@LB@ \| \|@LB@5'-UUA...ACACA UUU UGAU GUUAU...CCU-3'@LB@ GGACAUC GA AAGGCAG@LB@ \|\|\|\|\|\|\| \|\| \|\|:\|\|\|\|@LB@ CCUGUAG CU UUUCGUC@LB@3'-UUU...UUACC UUU ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -13.65 kcal/mol@LB@Hybridization Energy -19.0549 kcal/mol@LB@Unfolding Energy - mRNA 3.83037 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 190 -- 212@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 5 -- 11@LB@
125	0.009022	0.2491	b0658	ybeX	-16.01	0.015431	14 -- 34	5 -- 21	putative ion transport		_____________13____________________35\n_____________\|_____________________\|\n5'-UUA...CGAUC__________UGAC_______AAGAA...ACC-3'\n______________ACAUCGAAGA____GAAGCAG\n______________\|\|\|\|\|:\|\|\|\|____:\|\|\|\|\|\|\n______________UGUAGUUUCU____UUUCGUC\n3'-UUU...ACCCC_____________________ACCG-5'\n_____________\|_____________________\|\n_____________22____________________4\n	28 -- 34	5 -- 11	-20.2475 kcal/mol	2.73159 kcal/mol	1.5073 kcal/mol	13 35@LB@ \| \|@LB@5'-UUA...CGAUC UGAC AAGAA...ACC-3'@LB@ ACAUCGAAGA GAAGCAG@LB@ \|\|\|\|\|:\|\|\|\| :\|\|\|\|\|\|@LB@ UGUAGUUUCU UUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -16.01 kcal/mol@LB@Hybridization Energy -20.2475 kcal/mol@LB@Unfolding Energy - mRNA 2.73159 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 14 -- 34@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 5 -- 11@LB@
135	0.009724	0.2504	b1387	paaZ	-12.57	0.095542	174 -- 198	5 -- 30	oxepin-CoA hydrolase and 3-oxo-5 6-dehydrosuberyl-CoA semialdehyde dehydrogenase		_____________173_________________________199\n_____________\|___________________________\|\n5'-UAA...CAACA______U_AA_____U___________CGAUG...AAG-3'\n______________GAAAUG_G__ACAUC___GGAGAGUAG\n______________:\|\|\|\|\|_\|__\|\|\|\|\|___\|:\|:\|\|:\|\|\n______________UUUUAC_C__UGUAG___CUUUUCGUC\n3'-UUU...AGGUG________CC_____UUU_________ACCG-5'\n_____________\|___________________________\|\n_____________31__________________________4\n	192 -- 198	5 -- 11	-19.0129 kcal/mol	3.93627 kcal/mol	2.50278 kcal/mol	173 199@LB@ \| \|@LB@5'-UAA...CAACA U AA U CGAUG...AAG-3'@LB@ GAAAUG G ACAUC GGAGAGUAG@LB@ :\|\|\|\|\| \| \|\|\|\|\| \|:\|:\|\|:\|\|@LB@ UUUUAC C UGUAG CUUUUCGUC@LB@3'-UUU...AGGUG CC UUU ACCG-5'@LB@ \| \|@LB@ 31 4@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -19.0129 kcal/mol@LB@Unfolding Energy - mRNA 3.93627 kcal/mol@LB@Unfolding Energy - sRNA 2.50278 kcal/mol@LB@@LB@Position - mRNA 174 -- 198@LB@Position - sRNA 5 -- 30@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@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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