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
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@
14	0.0006392	0.1243	b3745	viaA	-13.90	0.050132	246 -- 264	10 -- 25	stimulator of RavA ATPase activity; von Willebrand factor domain protein		_____________245_________________265\n_____________\|___________________\|\n5'-ACG...GCGAA_A_____UG__________UGAUC...CGG-3'\n______________G_GGGAU__AUCGAAGAGA\n______________\|_\|\|\|\|:__\|\|\|:\|\|\|\|:\|\n______________C_CCCUG__UAGUUUCUUU\n3'-UUU...UUUUA___________________UCGUC...CCG-5'\n_____________\|___________________\|\n_____________26__________________9\n	258 -- 264	10 -- 16	-16.9183 kcal/mol	2.35086 kcal/mol	0.670388 kcal/mol	245 265@LB@ \| \|@LB@5'-ACG...GCGAA A UG UGAUC...CGG-3'@LB@ G GGGAU AUCGAAGAGA@LB@ \| \|\|\|\|: \|\|\|:\|\|\|\|:\|@LB@ C CCCUG UAGUUUCUUU@LB@3'-UUU...UUUUA UCGUC...CCG-5'@LB@ \| \|@LB@ 26 9@LB@@LB@@LB@Energy -13.90 kcal/mol@LB@Hybridization Energy -16.9183 kcal/mol@LB@Unfolding Energy - mRNA 2.35086 kcal/mol@LB@Unfolding Energy - sRNA 0.670388 kcal/mol@LB@@LB@Position - mRNA 246 -- 264@LB@Position - sRNA 10 -- 25@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 10 -- 16@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@
133	0.009634	0.2504	b2551	glyA	-13.83	0.051752	272 -- 286	6 -- 21	serine hydroxymethyltransferase		_____________271______________287\n_____________\|________________\|\n5'-CAA...AAAGU________________CAUCG...UCG-3'\n______________ACGUC_AGGAAGAGCA\n______________\|\|:\|\|_\|:\|\|\|:\|\|\|\|\n______________UGUAG_UUCUUUUCGU\n3'-UUU...ACCCC_____U__________CACCG-5'\n_____________\|________________\|\n_____________22_______________5\n	280 -- 286	6 -- 12	-16.7043 kcal/mol	2.28484 kcal/mol	0.584589 kcal/mol	271 287@LB@ \| \|@LB@5'-CAA...AAAGU CAUCG...UCG-3'@LB@ ACGUC AGGAAGAGCA@LB@ \|\|:\|\| \|:\|\|\|:\|\|\|\|@LB@ UGUAG UUCUUUUCGU@LB@3'-UUU...ACCCC U CACCG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -13.83 kcal/mol@LB@Hybridization Energy -16.7043 kcal/mol@LB@Unfolding Energy - mRNA 2.28484 kcal/mol@LB@Unfolding Energy - sRNA 0.584589 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 6 -- 12@LB@
178	0.01293	0.2504	b4258	valS	-13.78	0.053235	248 -- 266	1 -- 21	valyl-tRNA synthetase		_____________247___________________267\n_____________\|_____________________\|\n5'-AUC...UACGA_____U_______________UACUU...AAA-3'\n______________GCA_C_GGGAAAAGCAG_GGC\n______________:\|\|_\|_::\|\|\|\|\|\|\|\|\|_\|\|\|\n______________UGU_G_UUCUUUUCGUC_CCG\n3'-UUU...ACCCC___A_U___________A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	257 -- 263	5 -- 11	-22.196 kcal/mol	6.90555 kcal/mol	1.51103 kcal/mol	247 267@LB@ \| \|@LB@5'-AUC...UACGA U UACUU...AAA-3'@LB@ GCA C GGGAAAAGCAG GGC@LB@ :\|\| \| ::\|\|\|\|\|\|\|\|\| \|\|\|@LB@ UGU G UUCUUUUCGUC CCG@LB@3'-UUU...ACCCC A U A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.78 kcal/mol@LB@Hybridization Energy -22.196 kcal/mol@LB@Unfolding Energy - mRNA 6.90555 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 248 -- 266@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 5 -- 11@LB@
34	0.001647	0.1648	b1218	chaC	-13.74	0.054411	171 -- 189	1 -- 17	cation transport regulator		_____________170_________________190\n_____________\|___________________\|\n5'-AUA...UGUCG________UAU________GGAAG...CGC-3'\n______________CAGGGAAG___GCAGUGGC\n______________\|\|::\|\|\|:___\|\|\|\|\|\|\|\|\n______________GUUUCUUU___CGUCACCG\n3'-UUU...CUGUA________U__________-5'\n_____________\|__________________\|\n_____________18_________________1\n	183 -- 189	1 -- 7	-23.3292 kcal/mol	8.15416 kcal/mol	1.43853 kcal/mol	170 190@LB@ \| \|@LB@5'-AUA...UGUCG UAU GGAAG...CGC-3'@LB@ CAGGGAAG GCAGUGGC@LB@ \|\|::\|\|\|: \|\|\|\|\|\|\|\|@LB@ GUUUCUUU CGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.74 kcal/mol@LB@Hybridization Energy -23.3292 kcal/mol@LB@Unfolding Energy - mRNA 8.15416 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 171 -- 189@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 1 -- 7@LB@
43	0.00215	0.1648	b4268	idnK	-13.73	0.054596	180 -- 268	1 -- 79	D-gluconate kinase thermosensitive	b3437	_____________179______________________________________________________________________________________________269\n_____________\|________________________________________________________________________________________________\|\n5'-AGG...AGGUA___U______GGA______________________U_AAAGCUUUAUU_________GU____G_______UAAA_______UUGGU____A____UGCCG...AUG-3'\n______________AGA_GAUUCA___GAUUUU______AAAUGGCGGG_G___________UUGAUGGGC__UUCA_GGAGUGG____ACAUUAA_____AGCA__GGU\n______________\|:\|_:\|::\|\|___:\|::\|\|______\|\|\|\|\|\|\|\|\|\|_\|___________\|\|\|\|\|\|\|\|\|__\|:\|\|_::\|:\|\|\|____\|\|\|\|:\|\|_____\|\|\|\|__\|\|:\n______________UUU_UUGGGU___UUGGAA______UUUACCGCCC_C___________AACUACCCG__AGGU_UUUUACC____UGUAGUU_____UCGU__CCG\n___________3'-___U______AG_______CUUGGC______________________________________G_______CC_________UCUUU____CA___-5'\n______________\|______________________________________________________________________________________________\|\n______________79_____________________________________________________________________________________________1\n	249 -- 255	15 -- 21	-57.0668 kcal/mol	16.9855 kcal/mol	26.3515 kcal/mol	179 269@LB@ \| \|@LB@5'-AGG...AGGUA U GGA U AAAGCUUUAUU GU G UAAA UUGGU A UGCCG...AUG-3'@LB@ AGA GAUUCA GAUUUU AAAUGGCGGG G UUGAUGGGC UUCA GGAGUGG ACAUUAA AGCA GGU@LB@ \|:\| :\|::\|\| :\|::\|\| \|\|\|\|\|\|\|\|\|\| \| \|\|\|\|\|\|\|\|\| \|:\|\| ::\|:\|\|\| \|\|\|\|:\|\| \|\|\|\| \|\|:@LB@ UUU UUGGGU UUGGAA UUUACCGCCC C AACUACCCG AGGU UUUUACC UGUAGUU UCGU CCG@LB@ 3'- U AG CUUGGC G CC UCUUU CA -5'@LB@ \| \|@LB@ 79 1@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -57.0668 kcal/mol@LB@Unfolding Energy - mRNA 16.9855 kcal/mol@LB@Unfolding Energy - sRNA 26.3515 kcal/mol@LB@@LB@Position - mRNA 180 -- 268@LB@Position - sRNA 1 -- 79@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 15 -- 21@LB@
114	0.007692	0.2368	b0584	fepA	-13.71	0.055244	241 -- 265	1 -- 26	ferrienterobactin outer membrane transporter		_____________240________________________266\n_____________\|__________________________\|\n5'-GAA...CAAUC___________U____U____CA___ACAAG...ACG-3'\n______________UGGGGAU_UUA_GGGG_AGCG__GGC\n______________\|\|\|\|\|\|:_\|:\|_:\|::_\|\|\|:__\|\|\|\n______________ACCCCUG_AGU_UCUU_UCGU__CCG\n3'-UUU...GUUUU_______U___U____U____CA___-5'\n_____________\|_________________________\|\n_____________27________________________1\n	241 -- 247	20 -- 26	-24.8633 kcal/mol	8.63835 kcal/mol	2.51842 kcal/mol	240 266@LB@ \| \|@LB@5'-GAA...CAAUC U U CA ACAAG...ACG-3'@LB@ UGGGGAU UUA GGGG AGCG GGC@LB@ \|\|\|\|\|\|: \|:\| :\|:: \|\|\|: \|\|\|@LB@ ACCCCUG AGU UCUU UCGU CCG@LB@3'-UUU...GUUUU U U U CA -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -13.71 kcal/mol@LB@Hybridization Energy -24.8633 kcal/mol@LB@Unfolding Energy - mRNA 8.63835 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 241 -- 265@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 20 -- 26@LB@
100	0.006296	0.2188	b1321	ycjX	-13.69	0.055797	38 -- 45	18 -- 25	DUF463 family protein puatative P-loop NTPase		_____________37_______46\n_____________\|________\|\n5'-UGA...UAGUA________AGGUC...CAG-3'\n______________GGGGACAU\n______________\|\|\|\|\|\|\|\|\n______________CCCCUGUA\n3'-UUU...UUUUA________GUUUC...CCG-5'\n_____________\|________\|\n_____________26_______17\n	39 -- 45	18 -- 24	-15.5505 kcal/mol	1.21152 kcal/mol	0.65218 kcal/mol	37 46@LB@ \| \|@LB@5'-UGA...UAGUA AGGUC...CAG-3'@LB@ GGGGACAU@LB@ \|\|\|\|\|\|\|\|@LB@ CCCCUGUA@LB@3'-UUU...UUUUA GUUUC...CCG-5'@LB@ \| \|@LB@ 26 17@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -15.5505 kcal/mol@LB@Unfolding Energy - mRNA 1.21152 kcal/mol@LB@Unfolding Energy - sRNA 0.65218 kcal/mol@LB@@LB@Position - mRNA 38 -- 45@LB@Position - sRNA 18 -- 25@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 18 -- 24@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@

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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usability assessment

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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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