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
1	0	0	b3752	rbsK	-20.54	0.000534	137 -- 155	1 -- 21	ribokinase		_____________136___________________156\n_____________\|_____________________\|\n5'-GCA...GUGUA_____________________ACGCG...GUA-3'\n______________AUA_UAAAGAAAAGCAG_GGC\n______________\|:\|_:\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\n______________UGU_GUUUCUUUUCGUC_CCG\n3'-UUU...ACCCC___A_____________A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	146 -- 152	5 -- 11	-23.5677 kcal/mol	1.51892 kcal/mol	1.51103 kcal/mol	136 156@LB@ \| \|@LB@5'-GCA...GUGUA ACGCG...GUA-3'@LB@ AUA UAAAGAAAAGCAG GGC@LB@ \|:\| :\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|@LB@ UGU GUUUCUUUUCGUC CCG@LB@3'-UUU...ACCCC A A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -20.54 kcal/mol@LB@Hybridization Energy -23.5677 kcal/mol@LB@Unfolding Energy - mRNA 1.51892 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 137 -- 155@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 5 -- 11@LB@
2	5.107e-11	8.961e-08	b2314	dedD	-25.37	0.000001	176 -- 205	1 -- 30	membrane-anchored periplasmic protein involved in septation		_____________175_____________________________206\n_____________\|_______________________________\|\n5'-UUG...UCAUG______AUU______________________AAGUA...AUU-3'\n______________GAAGUG___GACG_CGAGGAGAAGCGGUGGC\n______________:\|\|:\|\|___\|\|\|:_\|:\|:\|\|:\|\|\|\|:\|\|\|\|\|\n______________UUUUAC___CUGU_GUUUCUUUUCGUCACCG\n3'-UUU...AGGUG______CC_____A_________________-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	199 -- 205	1 -- 7	-36.5756 kcal/mol	8.68219 kcal/mol	2.51911 kcal/mol	175 206@LB@ \| \|@LB@5'-UUG...UCAUG AUU AAGUA...AUU-3'@LB@ GAAGUG GACG CGAGGAGAAGCGGUGGC@LB@ :\|\|:\|\| \|\|\|: \|:\|:\|\|:\|\|\|\|:\|\|\|\|\|@LB@ UUUUAC CUGU GUUUCUUUUCGUCACCG@LB@3'-UUU...AGGUG CC A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -25.37 kcal/mol@LB@Hybridization Energy -36.5756 kcal/mol@LB@Unfolding Energy - mRNA 8.68219 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 176 -- 205@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 1 -- 7@LB@
3	3.973e-07	0.0004647	b0081	mraZ	-16.47	0.011640	172 -- 200	1 -- 32	RsmH methytransferase inhibitor		_____________171______________________________201\n_____________\|________________________________\|\n5'-GAU...GUGGG__________A___A_____U___________AUGUU...AAA-3'\n______________GCAAAGUGGG_AUA__GGGG_GAGGC__UGGC\n______________:\|\|\|\|:\|\|\|\|_\|:\|__:::\|_:\|:\|\|__\|\|\|\|\n______________UGUUUUACCC_UGU__UUUC_UUUCG__ACCG\n3'-UUU...CGAGG__________C___AG____U_____UC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	175 -- 181	23 -- 29	-28.2943 kcal/mol	9.28897 kcal/mol	2.53929 kcal/mol	171 201@LB@ \| \|@LB@5'-GAU...GUGGG A A U AUGUU...AAA-3'@LB@ GCAAAGUGGG AUA GGGG GAGGC UGGC@LB@ :\|\|\|\|:\|\|\|\| \|:\| :::\| :\|:\|\| \|\|\|\|@LB@ UGUUUUACCC UGU UUUC UUUCG ACCG@LB@3'-UUU...CGAGG C AG U UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -16.47 kcal/mol@LB@Hybridization Energy -28.2943 kcal/mol@LB@Unfolding Energy - mRNA 9.28897 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 172 -- 200@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 23 -- 29@LB@
4	1.99e-05	0.01653	b4255	rraB	-17.36	0.006479	180 -- 205	1 -- 23	protein inhibitor of RNase E		_____________179________________________206\n_____________\|__________________________\|\n5'-GAG...CGGCA_________GA____U____CA____AAACC...CCA-3'\n______________GGACAUUAA__GGAA_GAGC__UGGC\n______________\|\|\|\|\|\|:\|\|__:\|\|\|_:\|\|\|__\|\|\|\|\n______________CCUGUAGUU__UCUU_UUCG__ACCG\n3'-UUU...UUACC____________________UC____-5'\n_____________\|_________________________\|\n_____________24________________________1\n	182 -- 188	15 -- 21	-24.3176 kcal/mol	5.37332 kcal/mol	1.57928 kcal/mol	179 206@LB@ \| \|@LB@5'-GAG...CGGCA GA U CA AAACC...CCA-3'@LB@ GGACAUUAA GGAA GAGC UGGC@LB@ \|\|\|\|\|\|:\|\| :\|\|\| :\|\|\| \|\|\|\|@LB@ CCUGUAGUU UCUU UUCG ACCG@LB@3'-UUU...UUACC UC -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -17.36 kcal/mol@LB@Hybridization Energy -24.3176 kcal/mol@LB@Unfolding Energy - mRNA 5.37332 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 15 -- 21@LB@
5	2.356e-05	0.01653	b1123	potD	-19.53	0.001282	190 -- 207	9 -- 25	spermidine/putrescine ABC transporter periplasmic binding protein		_____________189________________208\n_____________\|__________________\|\n5'-GAC...ACACA____________U_____AAUGG...ACU-3'\n______________GGGGACGUUAAA_GAAAA\n______________\|\|\|\|\|\|:\|:\|\|\|_\|\|\|\|\|\n______________CCCCUGUAGUUU_CUUUU\n3'-UUU...UUUUA__________________CGUCACCG-5'\n_____________\|__________________\|\n_____________26_________________8\n	195 -- 201	14 -- 20	-22.5319 kcal/mol	2.32696 kcal/mol	0.671024 kcal/mol	189 208@LB@ \| \|@LB@5'-GAC...ACACA U AAUGG...ACU-3'@LB@ GGGGACGUUAAA GAAAA@LB@ \|\|\|\|\|\|:\|:\|\|\| \|\|\|\|\|@LB@ CCCCUGUAGUUU CUUUU@LB@3'-UUU...UUUUA CGUCACCG-5'@LB@ \| \|@LB@ 26 8@LB@@LB@@LB@Energy -19.53 kcal/mol@LB@Hybridization Energy -22.5319 kcal/mol@LB@Unfolding Energy - mRNA 2.32696 kcal/mol@LB@Unfolding Energy - sRNA 0.671024 kcal/mol@LB@@LB@Position - mRNA 190 -- 207@LB@Position - sRNA 9 -- 25@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 14 -- 20@LB@
6	9.344e-05	0.05465	b2215	ompC	-14.72	0.032428	133 -- 159	1 -- 28	outer membrane porin protein C	b0929 b0241 b1377	_____________132____________________________160\n_____________\|______________________________\|\n5'-AUC...UGAUU____A___UUA_____UAU___________AUAAA...AUC-3'\n______________AAUG_GGG___AUCAG______GCAGUGGC\n______________\|\|\|\|_\|\|\|___\|\|\|\|:______\|\|\|\|\|\|\|\|\n______________UUAC_CCC___UAGUU______CGUCACCG\n3'-UUU...GUGUU________UG______UCUUUU________-5'\n_____________\|_____________________________\|\n_____________29____________________________1\n	153 -- 159	1 -- 7	-26.8714 kcal/mol	9.63393 kcal/mol	2.519 kcal/mol	132 160@LB@ \| \|@LB@5'-AUC...UGAUU A UUA UAU AUAAA...AUC-3'@LB@ AAUG GGG AUCAG GCAGUGGC@LB@ \|\|\|\| \|\|\| \|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UUAC CCC UAGUU CGUCACCG@LB@3'-UUU...GUGUU UG UCUUUU -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -14.72 kcal/mol@LB@Hybridization Energy -26.8714 kcal/mol@LB@Unfolding Energy - mRNA 9.63393 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 133 -- 159@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 1 -- 7@LB@
7	0.0001218	0.05555	b1811	yoaH	-21.30	0.000256	259 -- 293	1 -- 35	UPF0181 family protein		_____________258__________________________________294\n_____________\|____________________________________\|\n5'-ACG...GCGGA____G___C__AU____________U______C___CAGGCAA-3'\n______________UCCA_GAA_UG__GGCA_CAAGGGA_GAGCAG_GGC\n______________\|\|\|\|_:\|\|_\|\|__\|:\|\|_\|\|\|:\|:\|_:\|\|\|\|\|_\|\|\|\n______________AGGU_UUU_AC__CUGU_GUUUCUU_UUCGUC_CCG\n3'-UUU...ACCCG____G___U__CC____A______________A___-5'\n_____________\|___________________________________\|\n_____________36__________________________________1\n	276 -- 282	11 -- 17	-33.9537 kcal/mol	7.61738 kcal/mol	5.03645 kcal/mol	258 294@LB@ \| \|@LB@5'-ACG...GCGGA G C AU U C CAGGCAA-3'@LB@ UCCA GAA UG GGCA CAAGGGA GAGCAG GGC@LB@ \|\|\|\| :\|\| \|\| \|:\|\| \|\|\|:\|:\| :\|\|\|\|\| \|\|\|@LB@ AGGU UUU AC CUGU GUUUCUU UUCGUC CCG@LB@3'-UUU...ACCCG G U CC A A -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -21.30 kcal/mol@LB@Hybridization Energy -33.9537 kcal/mol@LB@Unfolding Energy - mRNA 7.61738 kcal/mol@LB@Unfolding Energy - sRNA 5.03645 kcal/mol@LB@@LB@Position - mRNA 259 -- 293@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 11 -- 17@LB@
8	0.0001267	0.05555	b2697	alaS	-16.66	0.010303	247 -- 274	1 -- 35	alanyl-tRNA synthetase		_____________246_________________________________275\n_____________\|___________________________________\|\n5'-CCA...CUUUU_______UAA______________________U__CAGCA...ACG-3'\n______________UCCAUAG____GGGACAUCA______GGUAGU_GC\n______________\|\|\|\|:\|:____\|\|\|\|\|\|\|\|\|______:\|:\|\|\|_\|\|\n______________AGGUGUU____CCCUGUAGU______UCGUCA_CG\n3'-UUU...ACCCG_______UUAC_________UUCUUU______C__-5'\n_____________\|__________________________________\|\n_____________36_________________________________1\n	259 -- 265	16 -- 22	-29.5579 kcal/mol	7.86268 kcal/mol	5.03645 kcal/mol	246 275@LB@ \| \|@LB@5'-CCA...CUUUU UAA U CAGCA...ACG-3'@LB@ UCCAUAG GGGACAUCA GGUAGU GC@LB@ \|\|\|\|:\|: \|\|\|\|\|\|\|\|\| :\|:\|\|\| \|\|@LB@ AGGUGUU CCCUGUAGU UCGUCA CG@LB@3'-UUU...ACCCG UUAC UUCUUU C -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -16.66 kcal/mol@LB@Hybridization Energy -29.5579 kcal/mol@LB@Unfolding Energy - mRNA 7.86268 kcal/mol@LB@Unfolding Energy - sRNA 5.03645 kcal/mol@LB@@LB@Position - mRNA 247 -- 274@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 16 -- 22@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@
10	0.0003274	0.1087	b1020	phoH	-9.93	0.281763	74 -- 85	48 -- 59	ATP-binding protein; putative PhoH family P-loop ATPase		_____________73___________86\n_____________\|____________\|\n5'-AAU...AUGUC____________UUUUA...AAC-3'\n______________ACUGAAAUGGUG\n______________\|\|:\|\|\|\|\|\|\|:\|\n______________UGGCUUUACCGC\n3'-UUU...GAACU____________CCCAA...CCG-5'\n_____________\|____________\|\n_____________60___________47\n	79 -- 85	48 -- 54	-17.134 kcal/mol	3.24305 kcal/mol	3.96136 kcal/mol	73 86@LB@ \| \|@LB@5'-AAU...AUGUC UUUUA...AAC-3'@LB@ ACUGAAAUGGUG@LB@ \|\|:\|\|\|\|\|\|\|:\|@LB@ UGGCUUUACCGC@LB@3'-UUU...GAACU CCCAA...CCG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -17.134 kcal/mol@LB@Unfolding Energy - mRNA 3.24305 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 74 -- 85@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 48 -- 54@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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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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