Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
57	0.01201	0.6177	b2959	yggL	-9.33	0.056423	82 -- 92	47 -- 57	DUF469 family protein	_____________81__________93\n_____________\|___________\|\n5'-GUA...AAAAC___________CAAUG...CAU-3'\n______________CUGUCAGAGAG\n______________\|:\|\|\|\|:\|\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	86 -- 92	47 -- 53	-15.1623 kcal/mol	3.10124 kcal/mol	2.73556 kcal/mol	81 93@LB@ \| \|@LB@5'-GUA...AAAAC CAAUG...CAU-3'@LB@ CUGUCAGAGAG@LB@ \|:\|\|\|\|:\|\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -15.1623 kcal/mol@LB@Unfolding Energy - mRNA 3.10124 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 82 -- 92@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 47 -- 53@LB@
105	0.0216	0.6177	b2962	yggX	-9.20	0.059738	186 -- 194	45 -- 53	oxidative damage protective factor for iron-sulfur proteins	_____________185_______195\n_____________\|_________\|\n5'-UCA...GUCGA_________UGAUU...AGA-3'\n______________UAAAGAGGA\n______________:\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	188 -- 194	45 -- 51	-10.7665 kcal/mol	0.645872 kcal/mol	0.917553 kcal/mol	185 195@LB@ \| \|@LB@5'-UCA...GUCGA UGAUU...AGA-3'@LB@ UAAAGAGGA@LB@ :\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -10.7665 kcal/mol@LB@Unfolding Energy - mRNA 0.645872 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 45 -- 51@LB@
149	0.03014	0.6177	b4470	yhaM	-8.71	0.074988	251 -- 260	44 -- 54	putative L-serine dehydratase alpha chain	_____________250_________261\n_____________\|___________\|\n5'-UGU...GCCGU___________GUAAA...UGG-3'\n______________UC_AGGAGGAA\n______________\|\|_\|:\|\|\|\|\|\|\n______________AG_UUCUCCUU\n3'-UUU...CGGGC__U________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	254 -- 260	44 -- 50	-10.8529 kcal/mol	1.19981 kcal/mol	0.939671 kcal/mol	250 261@LB@ \| \|@LB@5'-UGU...GCCGU GUAAA...UGG-3'@LB@ UC AGGAGGAA@LB@ \|\| \|:\|\|\|\|\|\|@LB@ AG UUCUCCUU@LB@3'-UUU...CGGGC U AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -10.8529 kcal/mol@LB@Unfolding Energy - mRNA 1.19981 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 251 -- 260@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 44 -- 50@LB@
200	0.04173	0.6177	b3155	yhbQ	-7.74	0.117248	9 -- 16	50 -- 57	GIY-YIG nuclease superfamily protein	_____________8________17\n_____________\|________\|\n___5'-UUUUUCUU________AUGUA...GCG-3'\n______________CCGUCAAA\n______________\|\|\|\|\|\|\|\|\n______________GGCAGUUU\n3'-UUU...AACCG________CUCCU...ACA-5'\n_____________\|________\|\n_____________58_______49\n	10 -- 16	50 -- 56	-10.5697 kcal/mol	0.110673 kcal/mol	2.72137 kcal/mol	8 17@LB@ \| \|@LB@ 5'-UUUUUCUU AUGUA...GCG-3'@LB@ CCGUCAAA@LB@ \|\|\|\|\|\|\|\|@LB@ GGCAGUUU@LB@3'-UUU...AACCG CUCCU...ACA-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -10.5697 kcal/mol@LB@Unfolding Energy - mRNA 0.110673 kcal/mol@LB@Unfolding Energy - sRNA 2.72137 kcal/mol@LB@@LB@Position - mRNA 9 -- 16@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 10 -- 16@LB@Position Seed - sRNA 50 -- 56@LB@
132	0.02588	0.6177	b3180	yhbY	-5.98	0.252347	290 -- 297	46 -- 53	RNA binding protein associated with pre-50S ribosomal subunits	_____________289______298\n_____________\|________\|\n5'-CUG...UUGAC________UGC-3'\n______________CGAAGGGG\n______________\|:\|\|\|:\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	291 -- 297	46 -- 52	-10.2464 kcal/mol	3.35117 kcal/mol	0.910679 kcal/mol	289 298@LB@ \| \|@LB@5'-CUG...UUGAC UGC-3'@LB@ CGAAGGGG@LB@ \|:\|\|\|:\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -5.98 kcal/mol@LB@Hybridization Energy -10.2464 kcal/mol@LB@Unfolding Energy - mRNA 3.35117 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 46 -- 52@LB@
141	0.02753	0.6177	b3215	yhcA	-6.30	0.221284	185 -- 194	39 -- 48	putative periplasmic chaperone protein	_____________184________195\n_____________\|__________\|\n5'-ACG...AUUAC__________AUUUA...AAA-3'\n______________AGGAGUUUUA\n______________\|\|\|\|:\|\|\|:\|\n______________UCCUUAAAGU\n3'-UUU...GUUUC__________AAAAA...ACA-5'\n_____________\|__________\|\n_____________49_________38\n	187 -- 193	40 -- 46	-10.0044 kcal/mol	2.68942 kcal/mol	1.01866 kcal/mol	184 195@LB@ \| \|@LB@5'-ACG...AUUAC AUUUA...AAA-3'@LB@ AGGAGUUUUA@LB@ \|\|\|\|:\|\|\|:\|@LB@ UCCUUAAAGU@LB@3'-UUU...GUUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 49 38@LB@@LB@@LB@Energy -6.30 kcal/mol@LB@Hybridization Energy -10.0044 kcal/mol@LB@Unfolding Energy - mRNA 2.68942 kcal/mol@LB@Unfolding Energy - sRNA 1.01866 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 39 -- 48@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
172	0.03476	0.6177	b3441	yhhY	-9.34	0.055938	185 -- 193	45 -- 53	aminoacyl nucleotide detoxifying acetyltransferase	_____________184_______194\n_____________\|_________\|\n5'-CCC...UACCC_________CAAAG...UGC-3'\n______________CAAAGAGGA\n______________\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	187 -- 193	45 -- 51	-12.8083 kcal/mol	2.54681 kcal/mol	0.917553 kcal/mol	184 194@LB@ \| \|@LB@5'-CCC...UACCC CAAAG...UGC-3'@LB@ CAAAGAGGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -12.8083 kcal/mol@LB@Unfolding Energy - mRNA 2.54681 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 185 -- 193@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
93	0.01877	0.6177	b3492	yhiN	-6.30	0.220558	150 -- 160	43 -- 53	putative oxidoreductase	_____________149_________161\n_____________\|___________\|\n5'-CGG...GCGAC__CU_______CUUUA...AUA-3'\n______________CA__GAGGAAU\n______________\|\|__\|\|\|\|\|\|\|\n______________GU__CUCCUUA\n3'-UUU...GGGCA__UU_______AAGUA...ACA-5'\n_____________\|___________\|\n_____________54__________42\n	154 -- 160	43 -- 49	-10.7951 kcal/mol	3.55798 kcal/mol	0.933055 kcal/mol	149 161@LB@ \| \|@LB@5'-CGG...GCGAC CU CUUUA...AUA-3'@LB@ CA GAGGAAU@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU CUCCUUA@LB@3'-UUU...GGGCA UU AAGUA...ACA-5'@LB@ \| \|@LB@ 54 42@LB@@LB@@LB@Energy -6.30 kcal/mol@LB@Hybridization Energy -10.7951 kcal/mol@LB@Unfolding Energy - mRNA 3.55798 kcal/mol@LB@Unfolding Energy - sRNA 0.933055 kcal/mol@LB@@LB@Position - mRNA 150 -- 160@LB@Position - sRNA 43 -- 53@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 43 -- 49@LB@
135	0.02628	0.6177	b3547	yhjX	-9.70	0.047334	158 -- 184	28 -- 55	pyruvate-inducible inner membrane protein putative transporter	_____________157___________________________185\n_____________\|_____________________________\|\n5'-UAA...UGGUU_____C____AUU____C___________CUGCA...UUA-3'\n______________GUCGG_AGAG___UUUC___UUUUUAUUA\n______________\|\|\|::_\|\|\|\|___\|\|\|\|___\|\|\|\|\|\|\|\|\|\n______________CAGUU_UCUC___AAAG___AAAAAUAAU\n3'-UUU...CCGGG__________CUU____UAA_________AAUAC...ACA-5'\n_____________\|_____________________________\|\n_____________56____________________________27\n	178 -- 184	28 -- 34	-15.2509 kcal/mol	4.36169 kcal/mol	1.18814 kcal/mol	157 185@LB@ \| \|@LB@5'-UAA...UGGUU C AUU C CUGCA...UUA-3'@LB@ GUCGG AGAG UUUC UUUUUAUUA@LB@ \|\|\|:: \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CAGUU UCUC AAAG AAAAAUAAU@LB@3'-UUU...CCGGG CUU UAA AAUAC...ACA-5'@LB@ \| \|@LB@ 56 27@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -15.2509 kcal/mol@LB@Unfolding Energy - mRNA 4.36169 kcal/mol@LB@Unfolding Energy - sRNA 1.18814 kcal/mol@LB@@LB@Position - mRNA 158 -- 184@LB@Position - sRNA 28 -- 55@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 28 -- 34@LB@
39	0.007917	0.6129	b3657	yicJ	-11.19	0.023423	220 -- 230	47 -- 57	putative transporter	_____________219_________231\n_____________\|___________\|\n5'-CAG...GUUGU___________AAAAU...UGU-3'\n______________CCGUUAAAGAG\n______________\|\|\|\|:\|\|\|\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	224 -- 230	47 -- 53	-15.9196 kcal/mol	1.98973 kcal/mol	2.73556 kcal/mol	219 231@LB@ \| \|@LB@5'-CAG...GUUGU AAAAU...UGU-3'@LB@ CCGUUAAAGAG@LB@ \|\|\|\|:\|\|\|\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -15.9196 kcal/mol@LB@Unfolding Energy - mRNA 1.98973 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 220 -- 230@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 47 -- 53@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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