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
180	0.01303	0.2504	b3487	yhiI	-13.61	0.058128	230 -- 256	1 -- 27	putative membrane fusion protein (MFP) of efflux pump	_____________229__________________________257\n_____________\|____________________________\|\n5'-UUU...GCGUG_____U________UUACU_________GGCUA...CGG-3'\n______________GUGGG__UGUCGGG_____GGCGGUGGC\n______________:\|\|\|\|__::\|\|:::_____:\|\|:\|\|\|\|\|\n______________UACCC__GUAGUUU_____UCGUCACCG\n3'-UUU...UGUUU_____CU_______CUUU__________-5'\n_____________\|___________________________\|\n_____________28__________________________1\n	250 -- 256	1 -- 7	-27.1902 kcal/mol	11.0661 kcal/mol	2.51867 kcal/mol	229 257@LB@ \| \|@LB@5'-UUU...GCGUG U UUACU GGCUA...CGG-3'@LB@ GUGGG UGUCGGG GGCGGUGGC@LB@ :\|\|\|\| ::\|\|::: :\|\|:\|\|\|\|\|@LB@ UACCC GUAGUUU UCGUCACCG@LB@3'-UUU...UGUUU CU CUUU -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -27.1902 kcal/mol@LB@Unfolding Energy - mRNA 11.0661 kcal/mol@LB@Unfolding Energy - sRNA 2.51867 kcal/mol@LB@@LB@Position - mRNA 230 -- 256@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 1 -- 7@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@
191	0.01405	0.2529	b3532	bcsB	-12.45	0.101006	205 -- 235	1 -- 16	regulator of cellulose synthase cyclic di-GMP binding	_____________204_____________________________236\n_____________\|_______________________________\|\n5'-AAG...GAUGA________CUAUUCUGGAUUUGU________UAUGG...UCA-3'\n______________AAAGAAAA_______________GCAGUGGC\n______________\|\|\|\|\|\|\|\|_______________\|\|\|\|\|\|\|\|\n______________UUUCUUUU_______________CGUCACCG\n3'-UUU...UGUAG_______________________________-5'\n_____________\|______________________________\|\n_____________17_____________________________1\n	229 -- 235	1 -- 7	-19.2133 kcal/mol	5.41496 kcal/mol	1.34555 kcal/mol	204 236@LB@ \| \|@LB@5'-AAG...GAUGA CUAUUCUGGAUUUGU UAUGG...UCA-3'@LB@ AAAGAAAA GCAGUGGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUUCUUUU CGUCACCG@LB@3'-UUU...UGUAG -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -19.2133 kcal/mol@LB@Unfolding Energy - mRNA 5.41496 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 205 -- 235@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
101	0.006298	0.2188	b3549	tag	-14.94	0.028658	147 -- 165	3 -- 21	3-methyl-adenine DNA glycosylase I constitutive	_____________146__________________166\n_____________\|____________________\|\n5'-GCA...CCGAU_________________C__AAAUU...AAA-3'\n______________GCGUC_AAGAAAAGCGG_UG\n______________:\|:\|\|_\|\|\|\|\|\|\|\|\|:\|_\|\|\n______________UGUAG_UUCUUUUCGUC_AC\n3'-UUU...ACCCC_____U______________CG-5'\n_____________\|____________________\|\n_____________22___________________2\n	156 -- 162	5 -- 11	-20.7072 kcal/mol	4.25403 kcal/mol	1.5107 kcal/mol	146 166@LB@ \| \|@LB@5'-GCA...CCGAU C AAAUU...AAA-3'@LB@ GCGUC AAGAAAAGCGG UG@LB@ :\|:\|\| \|\|\|\|\|\|\|\|\|:\| \|\|@LB@ UGUAG UUCUUUUCGUC AC@LB@3'-UUU...ACCCC U CG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -20.7072 kcal/mol@LB@Unfolding Energy - mRNA 4.25403 kcal/mol@LB@Unfolding Energy - sRNA 1.5107 kcal/mol@LB@@LB@Position - mRNA 147 -- 165@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 5 -- 11@LB@
70	0.003861	0.1936	b3559	glyS	-15.28	0.023738	120 -- 130	1 -- 11	glycine tRNA synthetase beta subunit	_____________119_________131\n_____________\|___________\|\n5'-CGC...UGACC___________AGAAG...CGG-3'\n______________AAAGCAGUGGC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UUUCGUCACCG\n3'-UUU...UUUCU___________-5'\n_____________\|__________\|\n_____________12_________1\n	124 -- 130	1 -- 7	-20.0617 kcal/mol	3.50787 kcal/mol	1.27751 kcal/mol	119 131@LB@ \| \|@LB@5'-CGC...UGACC AGAAG...CGG-3'@LB@ AAAGCAGUGGC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UUUCGUCACCG@LB@3'-UUU...UUUCU -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -15.28 kcal/mol@LB@Hybridization Energy -20.0617 kcal/mol@LB@Unfolding Energy - mRNA 3.50787 kcal/mol@LB@Unfolding Energy - sRNA 1.27751 kcal/mol@LB@@LB@Position - mRNA 120 -- 130@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 1 -- 7@LB@
22	0.0008145	0.1243	b3574	yiaJ	-21.10	0.000313	196 -- 241	1 -- 32	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon	_____________195____________________________________________242\n_____________\|______________________________________________\|\n5'-CCC...ACGCG____________A_GAAGUGAUGGGAAAA________CG__A____GCAGG...UUG-3'\n______________ACAAAAUGGGGA_A_______________AAAGAGAA__AG_UGGC\n______________\|\|\|\|\|\|\|\|\|\|\|\|_\|_______________\|\|\|\|\|:\|\|__\|\|_\|\|\|\|\n______________UGUUUUACCCCU_U_______________UUUCUUUU__UC_ACCG\n3'-UUU...CGAGG____________G_AG_____________________CG_______-5'\n_____________\|_____________________________________________\|\n_____________33____________________________________________1\n	226 -- 232	9 -- 15	-30.0936 kcal/mol	6.45407 kcal/mol	2.53929 kcal/mol	195 242@LB@ \| \|@LB@5'-CCC...ACGCG A GAAGUGAUGGGAAAA CG A GCAGG...UUG-3'@LB@ ACAAAAUGGGGA A AAAGAGAA AG UGGC@LB@ \|\|\|\|\|\|\|\|\|\|\|\| \| \|\|\|\|\|:\|\| \|\| \|\|\|\|@LB@ UGUUUUACCCCU U UUUCUUUU UC ACCG@LB@3'-UUU...CGAGG G AG CG -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -21.10 kcal/mol@LB@Hybridization Energy -30.0936 kcal/mol@LB@Unfolding Energy - mRNA 6.45407 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 196 -- 241@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 9 -- 15@LB@
193	0.01407	0.2529	b3582	sgbU	-12.18	0.114391	219 -- 241	1 -- 24	putative L-xylulose 5-phosphate 3-epimerase	_____________218______________________242\n_____________\|________________________\|\n5'-UCU...AGUUA_________UGA_______C____GAAAG...UUG-3'\n______________GGGAU_UUA___AAAAGCG_UGGC\n______________\|\|\|\|:_\|:\|___\|\|\|\|\|\|:_\|\|\|\|\n______________CCCUG_AGU___UUUUCGU_ACCG\n3'-UUU...UUUAC_____U___UUC_______C____-5'\n_____________\|_______________________\|\n_____________25______________________1\n	230 -- 236	6 -- 12	-20.9157 kcal/mol	6.29567 kcal/mol	2.44282 kcal/mol	218 242@LB@ \| \|@LB@5'-UCU...AGUUA UGA C GAAAG...UUG-3'@LB@ GGGAU UUA AAAAGCG UGGC@LB@ \|\|\|\|: \|:\| \|\|\|\|\|\|: \|\|\|\|@LB@ CCCUG AGU UUUUCGU ACCG@LB@3'-UUU...UUUAC U UUC C -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -20.9157 kcal/mol@LB@Unfolding Energy - mRNA 6.29567 kcal/mol@LB@Unfolding Energy - sRNA 2.44282 kcal/mol@LB@@LB@Position - mRNA 219 -- 241@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 6 -- 12@LB@
103	0.006657	0.2268	b3617	kbl	-13.19	0.071337	258 -- 276	7 -- 25	glycine C-acetyltransferase	_____________257_________________277\n_____________\|___________________\|\n5'-UUU...CGGAA___UUGU____________GCAUU...AAG-3'\n______________GGG____UUAAAGAAGAGC\n______________\|\|\|____\|:\|\|\|\|\|\|:\|\|\|\n______________CCC____AGUUUCUUUUCG\n3'-UUU...UUUUA___CUGU____________UCACCG-5'\n_____________\|___________________\|\n_____________26__________________6\n	270 -- 276	7 -- 13	-19.594 kcal/mol	5.69693 kcal/mol	0.70626 kcal/mol	257 277@LB@ \| \|@LB@5'-UUU...CGGAA UUGU GCAUU...AAG-3'@LB@ GGG UUAAAGAAGAGC@LB@ \|\|\| \|:\|\|\|\|\|\|:\|\|\|@LB@ CCC AGUUUCUUUUCG@LB@3'-UUU...UUUUA CUGU UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -19.594 kcal/mol@LB@Unfolding Energy - mRNA 5.69693 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 258 -- 276@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 7 -- 13@LB@
165	0.01211	0.2504	b3642	pyrE	-11.74	0.138291	22 -- 41	7 -- 25	orotate phosphoribosyltransferase	_____________21___________________42\n_____________\|____________________\|\n5'-CGG...GUGCA_______GCA_____C____CGUUC...AUU-3'\n______________GGGGACG___GAAGG_GAGC\n______________\|\|\|\|\|\|:___:\|\|\|:_:\|\|\|\n______________CCCCUGU___UUUCU_UUCG\n3'-UUU...UUUUA_______AG______U____UCACCG-5'\n_____________\|____________________\|\n_____________26___________________6\n	22 -- 28	19 -- 25	-22.5653 kcal/mol	10.1153 kcal/mol	0.70626 kcal/mol	21 42@LB@ \| \|@LB@5'-CGG...GUGCA GCA C CGUUC...AUU-3'@LB@ GGGGACG GAAGG GAGC@LB@ \|\|\|\|\|\|: :\|\|\|: :\|\|\|@LB@ CCCCUGU UUUCU UUCG@LB@3'-UUU...UUUUA AG U UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -22.5653 kcal/mol@LB@Unfolding Energy - mRNA 10.1153 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 22 -- 41@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 19 -- 25@LB@
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@

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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