Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
88	0.008928	0.3104	b0405	queA	-8.89	0.184414	201 -- 209	5 -- 13	S-adenosylmethionine:tRNA ribosyltransferase-isomerase		_____________200_______210\n_____________\|_________\|\n5'-GGG...GUGUC_________ACCGA...GGC-3'\n______________AUGCGCGUU\n______________\|\|\|\|\|\|\|\|:\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	203 -- 209	5 -- 11	-14.1161 kcal/mol	4.07268 kcal/mol	1.15134 kcal/mol	200 210@LB@ \| \|@LB@5'-GGG...GUGUC ACCGA...GGC-3'@LB@ AUGCGCGUU@LB@ \|\|\|\|\|\|\|\|:@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -14.1161 kcal/mol@LB@Unfolding Energy - mRNA 4.07268 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 201 -- 209@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 5 -- 11@LB@
96	0.009671	0.3104	b0941	elfG	-12.70	0.041082	222 -- 232	5 -- 15	putative fimbrial-like adhesin protein	b3145 b0533	_____________221_________233\n_____________\|___________\|\n5'-UUU...GAGAA___________AUUAC...GGC-3'\n______________AAAUGCGUGUC\n______________\|\|\|\|\|\|\|:\|\|\|\n______________UUUACGCGCAG\n3'-UUU...UAUUG___________AAAG-5'\n_____________\|___________\|\n_____________16__________4\n	226 -- 232	5 -- 11	-17.0283 kcal/mol	3.13128 kcal/mol	1.19708 kcal/mol	221 233@LB@ \| \|@LB@5'-UUU...GAGAA AUUAC...GGC-3'@LB@ AAAUGCGUGUC@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ UUUACGCGCAG@LB@3'-UUU...UAUUG AAAG-5'@LB@ \| \|@LB@ 16 4@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -17.0283 kcal/mol@LB@Unfolding Energy - mRNA 3.13128 kcal/mol@LB@Unfolding Energy - sRNA 1.19708 kcal/mol@LB@@LB@Position - mRNA 222 -- 232@LB@Position - sRNA 5 -- 15@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 5 -- 11@LB@
100	0.01004	0.3104	b3166	truB	-9.42	0.151044	113 -- 128	5 -- 18	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase		_____________112______________129\n_____________\|________________\|\n5'-GGC...GGUUG__G________AU___AAACC...AAC-3'\n______________AA_GGAUGCGC__GUC\n______________\|\|_::\|\|\|\|\|\|__\|\|\|\n______________UU_UUUACGCG__CAG\n3'-UUU...UACUA__G_____________AAAG-5'\n_____________\|________________\|\n_____________19_______________4\n	117 -- 123	8 -- 14	-15.4757 kcal/mol	4.82661 kcal/mol	1.2243 kcal/mol	112 129@LB@ \| \|@LB@5'-GGC...GGUUG G AU AAACC...AAC-3'@LB@ AA GGAUGCGC GUC@LB@ \|\| ::\|\|\|\|\|\| \|\|\|@LB@ UU UUUACGCG CAG@LB@3'-UUU...UACUA G AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -15.4757 kcal/mol@LB@Unfolding Energy - mRNA 4.82661 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 113 -- 128@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 8 -- 14@LB@
101	0.01005	0.3104	b3288	fmt	-10.27	0.109217	249 -- 255	5 -- 11	10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase		_____________248_____256\n_____________\|_______\|\n5'-AUU...UUGCA_______AUCUC...UGU-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	249 -- 255	5 -- 11	-14.5658 kcal/mol	3.18739 kcal/mol	1.11145 kcal/mol	248 256@LB@ \| \|@LB@5'-AUU...UUGCA AUCUC...UGU-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -14.5658 kcal/mol@LB@Unfolding Energy - mRNA 3.18739 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 249 -- 255@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 5 -- 11@LB@
103	0.01026	0.3104	b1083	flgL	-8.46	0.215699	195 -- 209	5 -- 21	flagellar hook-filament junction protein		_____________194_______________210\n_____________\|_________________\|\n5'-UUG...GGGGA______________U__AGUAC...GUA-3'\n______________GAUAA__GAUGCGU_UC\n______________\|\|\|\|\|__:\|\|\|\|\|:_\|\|\n______________CUAUU__UUACGCG_AG\n3'-UUU...UACUA_____GU_______C__AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	200 -- 206	8 -- 14	-13.0743 kcal/mol	3.36074 kcal/mol	1.24955 kcal/mol	194 210@LB@ \| \|@LB@5'-UUG...GGGGA U AGUAC...GUA-3'@LB@ GAUAA GAUGCGU UC@LB@ \|\|\|\|\| :\|\|\|\|\|: \|\|@LB@ CUAUU UUACGCG AG@LB@3'-UUU...UACUA GU C AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -13.0743 kcal/mol@LB@Unfolding Energy - mRNA 3.36074 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 195 -- 209@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@LB@
104	0.01032	0.3104	b1714	pheS	-13.82	0.025875	273 -- 287	5 -- 21	phenylalanine tRNA synthetase alpha subunit		_____________272_______________288\n_____________\|_________________\|\n5'-UUG...CGUUA_________________GAAUA...GUA-3'\n______________GAUAAU__GUGCGCGUC\n______________\|\|\|\|\|:__:\|\|\|\|\|\|\|\|\n______________CUAUUG__UACGCGCAG\n3'-UUU...UACUA______UU_________AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	281 -- 287	5 -- 11	-20.2911 kcal/mol	5.22554 kcal/mol	1.24955 kcal/mol	272 288@LB@ \| \|@LB@5'-UUG...CGUUA GAAUA...GUA-3'@LB@ GAUAAU GUGCGCGUC@LB@ \|\|\|\|\|: :\|\|\|\|\|\|\|\|@LB@ CUAUUG UACGCGCAG@LB@3'-UUU...UACUA UU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -20.2911 kcal/mol@LB@Unfolding Energy - mRNA 5.22554 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 273 -- 287@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 5 -- 11@LB@
106	0.0109	0.3104	b2510	yfgJ	-10.53	0.098521	243 -- 261	5 -- 21	DUF1407 family protein		_____________242_________________262\n_____________\|___________________\|\n5'-UAA...AUCAG________CC_________GCCGA...UUU-3'\n______________GAUAACGG__AUGCGCGUU\n______________\|\|\|\|\|\|::__\|\|\|\|\|\|\|\|:\n______________CUAUUGUU__UACGCGCAG\n3'-UUU...UACUA___________________AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	255 -- 261	5 -- 11	-20.9599 kcal/mol	9.18032 kcal/mol	1.24955 kcal/mol	242 262@LB@ \| \|@LB@5'-UAA...AUCAG CC GCCGA...UUU-3'@LB@ GAUAACGG AUGCGCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|\|\|\|:@LB@ CUAUUGUU UACGCGCAG@LB@3'-UUU...UACUA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -20.9599 kcal/mol@LB@Unfolding Energy - mRNA 9.18032 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 5 -- 11@LB@
108	0.01118	0.3104	b2565	recO	-9.71	0.135448	294 -- 300	5 -- 11	gap repair protein		_____________293____300\n_____________\|______\|\n5'-GAA...GGCGC_______-3'\n______________GUGCGUC\n______________\|:\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	294 -- 300	5 -- 11	-11.8762 kcal/mol	1.05403 kcal/mol	1.11145 kcal/mol	293 300@LB@ \| \|@LB@5'-GAA...GGCGC -3'@LB@ GUGCGUC@LB@ \|:\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -11.8762 kcal/mol@LB@Unfolding Energy - mRNA 1.05403 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 294 -- 300@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 5 -- 11@LB@
117	0.01191	0.3104	b2137	yohF	-11.08	0.079147	231 -- 259	5 -- 35	putative oxidoreductase		_____________230_____________________________260\n_____________\|_______________________________\|\n5'-UAA...CCUCC___________C____CAAA___________AUUAC...GGC-3'\n______________GAUUCGGGGAU___GG____GAGUGCGCGUU\n______________:\|\|\|\|:\|\|\|\|\|___\|:____:\|:\|\|\|\|\|\|\|:\n______________UUAAGUCCCUA___CU____UUUACGCGCAG\n3'-UUU...GAGAC___________CUA__AUUG___________AAAG-5'\n_____________\|_______________________________\|\n_____________36______________________________4\n	253 -- 259	5 -- 11	-31.497 kcal/mol	11.2631 kcal/mol	9.15134 kcal/mol	230 260@LB@ \| \|@LB@5'-UAA...CCUCC C CAAA AUUAC...GGC-3'@LB@ GAUUCGGGGAU GG GAGUGCGCGUU@LB@ :\|\|\|\|:\|\|\|\|\| \|: :\|:\|\|\|\|\|\|\|:@LB@ UUAAGUCCCUA CU UUUACGCGCAG@LB@3'-UUU...GAGAC CUA AUUG AAAG-5'@LB@ \| \|@LB@ 36 4@LB@@LB@@LB@Energy -11.08 kcal/mol@LB@Hybridization Energy -31.497 kcal/mol@LB@Unfolding Energy - mRNA 11.2631 kcal/mol@LB@Unfolding Energy - sRNA 9.15134 kcal/mol@LB@@LB@Position - mRNA 231 -- 259@LB@Position - sRNA 5 -- 35@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 5 -- 11@LB@
129	0.01261	0.3104	b3025	qseB	-10.92	0.084347	141 -- 152	5 -- 17	quorum sensing DNA-binding response regulator in two-component regulatory system with QseC		_____________140___________153\n_____________\|_____________\|\n5'-GUG...GCUGU_____________ACAAC...GUC-3'\n______________ACAGA_GCGCGUU\n______________\|\|\|:\|_\|\|\|\|\|\|:\n______________UGUUU_CGCGCAG\n3'-UUU...ACUAU_____A_______AAAG-5'\n_____________\|_____________\|\n_____________18____________4\n	146 -- 152	5 -- 11	-15.7823 kcal/mol	3.63703 kcal/mol	1.22241 kcal/mol	140 153@LB@ \| \|@LB@5'-GUG...GCUGU ACAAC...GUC-3'@LB@ ACAGA GCGCGUU@LB@ \|\|\|:\| \|\|\|\|\|\|:@LB@ UGUUU CGCGCAG@LB@3'-UUU...ACUAU A AAAG-5'@LB@ \| \|@LB@ 18 4@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -15.7823 kcal/mol@LB@Unfolding Energy - mRNA 3.63703 kcal/mol@LB@Unfolding Energy - sRNA 1.22241 kcal/mol@LB@@LB@Position - mRNA 141 -- 152@LB@Position - sRNA 5 -- 17@LB@Position Seed - mRNA 146 -- 152@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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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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