Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
196	0.0344	0.5559	b0954	fabA	-7.50	0.274211	100 -- 110	74 -- 84	beta-hydroxydecanoyl thioester dehydrase	_____________99__________111\n_____________\|___________\|\n5'-GUG...GGCCA___________GAACU...ACA-3'\n______________UUACGUUGGCU\n______________\|:\|\|\|\|\|\|\|\|\|\n______________AGUGCAACCGA\n3'-CGC...UUUCA___________AAUCA...AAG-5'\n_____________\|___________\|\n_____________85__________73\n	104 -- 110	74 -- 80	-16.8122 kcal/mol	8.80896 kcal/mol	0.508159 kcal/mol	99 111@LB@ \| \|@LB@5'-GUG...GGCCA GAACU...ACA-3'@LB@ UUACGUUGGCU@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ AGUGCAACCGA@LB@3'-CGC...UUUCA AAUCA...AAG-5'@LB@ \| \|@LB@ 85 73@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -16.8122 kcal/mol@LB@Unfolding Energy - mRNA 8.80896 kcal/mol@LB@Unfolding Energy - sRNA 0.508159 kcal/mol@LB@@LB@Position - mRNA 100 -- 110@LB@Position - sRNA 74 -- 84@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 74 -- 80@LB@
5	0.0009313	0.5385	b3829	metE	-12.51	0.038445	233 -- 242	75 -- 84	5-methyltetrahydropteroyltriglutamate- homocysteine S-methyltransferase	_____________232________243\n_____________\|__________\|\n5'-GAG...UUCCC__________CUGCG...GUG-3'\n______________UCGCGUUGGC\n______________\|\|:\|\|\|\|\|\|\|\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	236 -- 242	75 -- 81	-17.7887 kcal/mol	4.77726 kcal/mol	0.505918 kcal/mol	232 243@LB@ \| \|@LB@5'-GAG...UUCCC CUGCG...GUG-3'@LB@ UCGCGUUGGC@LB@ \|\|:\|\|\|\|\|\|\|@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -12.51 kcal/mol@LB@Hybridization Energy -17.7887 kcal/mol@LB@Unfolding Energy - mRNA 4.77726 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 233 -- 242@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 75 -- 81@LB@
9	0.0016	0.5385	b1709	btuD	-9.25	0.141890	185 -- 194	75 -- 84	vitamin B12 ABC transporter ATPase	_____________184________195\n_____________\|__________\|\n5'-GCA...UAAAC_G________AAAAU...GGC-3'\n______________U_GCGUUGGC\n______________\|_:\|\|\|\|\|\|\|\n______________A_UGCAACCG\n3'-CGC...UUUCA_G________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	188 -- 194	75 -- 81	-15.1998 kcal/mol	5.44246 kcal/mol	0.505918 kcal/mol	184 195@LB@ \| \|@LB@5'-GCA...UAAAC G AAAAU...GGC-3'@LB@ U GCGUUGGC@LB@ \| :\|\|\|\|\|\|\|@LB@ A UGCAACCG@LB@3'-CGC...UUUCA G AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -15.1998 kcal/mol@LB@Unfolding Energy - mRNA 5.44246 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 75 -- 81@LB@
11	0.002269	0.5385	b1205	ychH	-11.36	0.061344	181 -- 195	75 -- 90	DUF2583 family putative inner membrane protein	_____________180______________196\n_____________\|________________\|\n5'-CAA...ACCCA___________GA___GACAU...UAC-3'\n______________GAAAGUUC_CG__GGU\n______________:\|\|\|\|\|\|\|_\|\|__\|\|:\n______________UUUUCAAG_GC__CCG\n3'-CGC...AGGCG________U__AA___AAAUC...AAG-5'\n_____________\|________________\|\n_____________91_______________74\n	182 -- 188	83 -- 89	-14.0006 kcal/mol	2.12575 kcal/mol	0.517251 kcal/mol	180 196@LB@ \| \|@LB@5'-CAA...ACCCA GA GACAU...UAC-3'@LB@ GAAAGUUC CG GGU@LB@ :\|\|\|\|\|\|\| \|\| \|\|:@LB@ UUUUCAAG GC CCG@LB@3'-CGC...AGGCG U AA AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -14.0006 kcal/mol@LB@Unfolding Energy - mRNA 2.12575 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 181 -- 195@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 83 -- 89@LB@
20	0.003438	0.5385	b3093	exuT	-11.51	0.057623	213 -- 228	75 -- 90	hexuronate transporter	_____________212______________229\n_____________\|________________\|\n5'-GGA...AAAUU_____G__________AUAUG...CGC-3'\n______________AAAGG_UUACGUUGGU\n______________\|\|\|:\|_\|:\|\|\|\|\|\|\|:\n______________UUUUC_AGUGCAACCG\n3'-CGC...AGGCG_____A__________AAAUC...AAG-5'\n_____________\|________________\|\n_____________91_______________74\n	222 -- 228	75 -- 81	-17.0017 kcal/mol	4.97243 kcal/mol	0.517251 kcal/mol	212 229@LB@ \| \|@LB@5'-GGA...AAAUU G AUAUG...CGC-3'@LB@ AAAGG UUACGUUGGU@LB@ \|\|\|:\| \|:\|\|\|\|\|\|\|:@LB@ UUUUC AGUGCAACCG@LB@3'-CGC...AGGCG A AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -17.0017 kcal/mol@LB@Unfolding Energy - mRNA 4.97243 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 213 -- 228@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 75 -- 81@LB@
22	0.004141	0.5385	b0462	acrB	-13.08	0.030428	256 -- 265	75 -- 84	multidrug efflux system protein	_____________255________266\n_____________\|__________\|\n5'-AAG...UAUCA__________AGGGG...CGC-3'\n______________UCAUGUUGGC\n______________\|\|\|:\|\|\|\|\|\|\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	259 -- 265	75 -- 81	-16.8887 kcal/mol	3.30616 kcal/mol	0.505918 kcal/mol	255 266@LB@ \| \|@LB@5'-AAG...UAUCA AGGGG...CGC-3'@LB@ UCAUGUUGGC@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -16.8887 kcal/mol@LB@Unfolding Energy - mRNA 3.30616 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 256 -- 265@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 75 -- 81@LB@
62	0.01254	0.5385	b0027	lspA	-10.68	0.080768	51 -- 66	75 -- 90	prolipoprotein signal peptidase (signal peptidase II)	_____________50________________67\n_____________\|_________________\|\n5'-UAU...GGGCU______________A__AAAGC...ACU-3'\n______________GAAAG_UCGCGUUG_GU\n______________:\|\|\|\|_\|\|:\|\|\|\|\|_\|:\n______________UUUUC_AGUGCAAC_CG\n3'-CGC...AGGCG_____A___________AAAUC...AAG-5'\n_____________\|_________________\|\n_____________91________________74\n	57 -- 63	77 -- 83	-15.4073 kcal/mol	4.21469 kcal/mol	0.517251 kcal/mol	50 67@LB@ \| \|@LB@5'-UAU...GGGCU A AAAGC...ACU-3'@LB@ GAAAG UCGCGUUG GU@LB@ :\|\|\|\| \|\|:\|\|\|\|\| \|:@LB@ UUUUC AGUGCAAC CG@LB@3'-CGC...AGGCG A AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -15.4073 kcal/mol@LB@Unfolding Energy - mRNA 4.21469 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 51 -- 66@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 57 -- 63@LB@Position Seed - sRNA 77 -- 83@LB@
66	0.01284	0.5385	b1645	ydhK	-10.57	0.084210	155 -- 164	75 -- 84	putative efflux protein (PET) component of YdhJK efflux pump	_____________154________165\n_____________\|__________\|\n5'-CAG...CGAUG__________GUCGG...UGG-3'\n______________UCACGUUGGU\n______________\|\|\|\|\|\|\|\|\|:\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	158 -- 164	75 -- 81	-15.7281 kcal/mol	4.6508 kcal/mol	0.505918 kcal/mol	154 165@LB@ \| \|@LB@5'-CAG...CGAUG GUCGG...UGG-3'@LB@ UCACGUUGGU@LB@ \|\|\|\|\|\|\|\|\|:@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -15.7281 kcal/mol@LB@Unfolding Energy - mRNA 4.6508 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 155 -- 164@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 75 -- 81@LB@
93	0.01594	0.5385	b3430	glgC	-8.76	0.171477	231 -- 238	75 -- 82	glucose-1-phosphate adenylyltransferase	_____________230______239\n_____________\|________\|\n5'-CAG...ACUUA________GCGCC...UGA-3'\n______________AUGUUGGC\n______________\|:\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	232 -- 238	75 -- 81	-11.9398 kcal/mol	2.84031 kcal/mol	0.339284 kcal/mol	230 239@LB@ \| \|@LB@5'-CAG...ACUUA GCGCC...UGA-3'@LB@ AUGUUGGC@LB@ \|:\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.9398 kcal/mol@LB@Unfolding Energy - mRNA 2.84031 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 231 -- 238@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 75 -- 81@LB@
94	0.01616	0.5385	b4217	ytfK	-8.94	0.160287	283 -- 290	75 -- 82	DUF1107 family protein	_____________282______291\n_____________\|________\|\n5'-GAA...CAAGG________GCUUU...AAU-3'\n______________ACGUUGGC\n______________\|\|\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	284 -- 290	75 -- 81	-13.4875 kcal/mol	4.21202 kcal/mol	0.339284 kcal/mol	282 291@LB@ \| \|@LB@5'-GAA...CAAGG GCUUU...AAU-3'@LB@ ACGUUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -13.4875 kcal/mol@LB@Unfolding Energy - mRNA 4.21202 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 283 -- 290@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 75 -- 81@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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