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
141	0.01345	0.3104	b3311	rpsQ	-8.13	0.242987	140 -- 150	8 -- 18	30S ribosomal subunit protein S17	_____________139_________151\n_____________\|___________\|\n5'-GGU...GUUGA___________CGCGA...UCU-3'\n______________AGCAAGUGCGU\n______________\|:\|\|\|:\|\|\|\|:\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	144 -- 150	8 -- 14	-14.6725 kcal/mol	5.33741 kcal/mol	1.20363 kcal/mol	139 151@LB@ \| \|@LB@5'-GGU...GUUGA CGCGA...UCU-3'@LB@ AGCAAGUGCGU@LB@ \|:\|\|\|:\|\|\|\|:@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -8.13 kcal/mol@LB@Hybridization Energy -14.6725 kcal/mol@LB@Unfolding Energy - mRNA 5.33741 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 140 -- 150@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 8 -- 14@LB@
70	0.006501	0.3087	b3301	rplO	-9.96	0.122936	194 -- 206	8 -- 20	50S ribosomal subunit protein L15	_____________193___________207\n_____________\|_____________\|\n5'-UUC...GAGGA____G________UUAAA...GUG-3'\n______________GUAA_AGAUGCGU\n______________:\|\|\|_\|:\|\|\|\|\|:\n______________UAUU_UUUACGCG\n3'-UUU...ACUAC____G________CAGAAAG-5'\n_____________\|_____________\|\n_____________21____________7\n	200 -- 206	8 -- 14	-13.6668 kcal/mol	2.47062 kcal/mol	1.23367 kcal/mol	193 207@LB@ \| \|@LB@5'-UUC...GAGGA G UUAAA...GUG-3'@LB@ GUAA AGAUGCGU@LB@ :\|\|\| \|:\|\|\|\|\|:@LB@ UAUU UUUACGCG@LB@3'-UUU...ACUAC G CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -9.96 kcal/mol@LB@Hybridization Energy -13.6668 kcal/mol@LB@Unfolding Energy - mRNA 2.47062 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 194 -- 206@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@LB@
197	0.01929	0.3104	b2185	rplY	-8.58	0.206984	8 -- 20	7 -- 19	50S ribosomal subunit protein L25	_____________7_____________21\n_____________\|_____________\|\n____5'-CCAGUAC_____________AAAAA...GCA-3'\n______________UGGCAGGUGCGUG\n______________\|::\|\|::\|\|\|\|:\|\n______________AUUGUUUACGCGC\n3'-UUU...CUACU_____________AGAAAG-5'\n_____________\|_____________\|\n_____________20____________6\n	14 -- 20	7 -- 13	-17.3397 kcal/mol	7.54262 kcal/mol	1.21943 kcal/mol	7 21@LB@ \| \|@LB@ 5'-CCAGUAC AAAAA...GCA-3'@LB@ UGGCAGGUGCGUG@LB@ \|::\|\|::\|\|\|\|:\|@LB@ AUUGUUUACGCGC@LB@3'-UUU...CUACU AGAAAG-5'@LB@ \| \|@LB@ 20 6@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -17.3397 kcal/mol@LB@Unfolding Energy - mRNA 7.54262 kcal/mol@LB@Unfolding Energy - sRNA 1.21943 kcal/mol@LB@@LB@Position - mRNA 8 -- 20@LB@Position - sRNA 7 -- 19@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 7 -- 13@LB@
195	0.01912	0.3104	b3910	yiiM	-10.43	0.102344	196 -- 205	9 -- 18	6-N-hydroxylaminopurine resistance protein	_____________195________206\n_____________\|__________\|\n5'-UAA...GAGGG__________AUAUC...UGC-3'\n______________AACAGAUGCG\n______________\|\|\|\|:\|\|\|\|\|\n______________UUGUUUACGC\n3'-UUU...UACUA__________GCAGAAAG-5'\n_____________\|__________\|\n_____________19_________8\n	199 -- 205	9 -- 15	-13.3675 kcal/mol	1.73119 kcal/mol	1.20319 kcal/mol	195 206@LB@ \| \|@LB@5'-UAA...GAGGG AUAUC...UGC-3'@LB@ AACAGAUGCG@LB@ \|\|\|\|:\|\|\|\|\|@LB@ UUGUUUACGC@LB@3'-UUU...UACUA GCAGAAAG-5'@LB@ \| \|@LB@ 19 8@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -13.3675 kcal/mol@LB@Unfolding Energy - mRNA 1.73119 kcal/mol@LB@Unfolding Energy - sRNA 1.20319 kcal/mol@LB@@LB@Position - mRNA 196 -- 205@LB@Position - sRNA 9 -- 18@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 9 -- 15@LB@
109	0.01118	0.3104	b3195	mlaF	-11.81	0.058997	89 -- 105	1 -- 18	ABC transporter maintaining OM lipid asymmetry ATP-binding protein	_____________88_________________106\n_____________\|__________________\|\n5'-UUU...AGUAA___________AG_____GCUAA...GAG-3'\n______________AACAAAUGC_C__CUUUC\n______________\|\|\|\|\|\|\|\|\|_\|__\|\|\|\|\|\n______________UUGUUUACG_G__GAAAG\n3'-UUU...UACUA_________C_CA_____-5'\n_____________\|_________________\|\n_____________19________________1\n	91 -- 97	10 -- 16	-16.9522 kcal/mol	3.89814 kcal/mol	1.24077 kcal/mol	88 106@LB@ \| \|@LB@5'-UUU...AGUAA AG GCUAA...GAG-3'@LB@ AACAAAUGC C CUUUC@LB@ \|\|\|\|\|\|\|\|\| \| \|\|\|\|\|@LB@ UUGUUUACG G GAAAG@LB@3'-UUU...UACUA C CA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -16.9522 kcal/mol@LB@Unfolding Energy - mRNA 3.89814 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 89 -- 105@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 10 -- 16@LB@
153	0.0145	0.3104	b3866	yihI	-12.31	0.048207	234 -- 252	5 -- 21	activator of Der GTPase	_____________233_________________253\n_____________\|___________________\|\n5'-GAA...GCAAA___CAU_____A_______GAAAA...GUC-3'\n______________GGU___GCAAA_GCGCGUC\n______________\|:\|___:\|\|\|\|_\|\|\|\|\|\|\|\n______________CUA___UGUUU_CGCGCAG\n3'-UUU...UACUA___U_______A_______AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	246 -- 252	5 -- 11	-18.8767 kcal/mol	5.31745 kcal/mol	1.24955 kcal/mol	233 253@LB@ \| \|@LB@5'-GAA...GCAAA CAU A GAAAA...GUC-3'@LB@ GGU GCAAA GCGCGUC@LB@ \|:\| :\|\|\|\| \|\|\|\|\|\|\|@LB@ CUA UGUUU CGCGCAG@LB@3'-UUU...UACUA U A AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -12.31 kcal/mol@LB@Hybridization Energy -18.8767 kcal/mol@LB@Unfolding Energy - mRNA 5.31745 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 234 -- 252@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 5 -- 11@LB@
81	0.007385	0.3087	b0736	ybgC	-11.71	0.061637	220 -- 237	4 -- 21	acyl-CoA thioester hydrolase	_____________219________________238\n_____________\|__________________\|\n5'-UUG...GUUUC______C___U_______ACUAU...AAA-3'\n______________GAUGGC_GGU_CGCGUCU\n______________\|\|\|::\|_::\|_\|\|\|\|\|\|\|\n______________CUAUUG_UUA_GCGCAGA\n3'-UUU...UACUA______U___C_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	231 -- 237	4 -- 10	-19.027 kcal/mol	6.06673 kcal/mol	1.2552 kcal/mol	219 238@LB@ \| \|@LB@5'-UUG...GUUUC C U ACUAU...AAA-3'@LB@ GAUGGC GGU CGCGUCU@LB@ \|\|\|::\| ::\| \|\|\|\|\|\|\|@LB@ CUAUUG UUA GCGCAGA@LB@3'-UUU...UACUA U C AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -19.027 kcal/mol@LB@Unfolding Energy - mRNA 6.06673 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 220 -- 237@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 4 -- 10@LB@
198	0.0193	0.3104	b2961	mutY	-10.33	0.106403	22 -- 38	1 -- 15	adenine DNA glycosylase	_____________21________________39\n_____________\|_________________\|\n5'-CGU...CGGUG_____A__U________AUAAA...UAU-3'\n______________AAAUG_CG_CGUUUUUC\n______________\|\|\|\|\|_\|\|_\|\|\|:\|\|\|\|\n______________UUUAC_GC_GCAGAAAG\n3'-UUU...UAUUG_________________-5'\n_____________\|________________\|\n_____________16_______________1\n	32 -- 38	1 -- 7	-14.8981 kcal/mol	3.3462 kcal/mol	1.21803 kcal/mol	21 39@LB@ \| \|@LB@5'-CGU...CGGUG A U AUAAA...UAU-3'@LB@ AAAUG CG CGUUUUUC@LB@ \|\|\|\|\| \|\| \|\|\|:\|\|\|\|@LB@ UUUAC GC GCAGAAAG@LB@3'-UUU...UAUUG -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -14.8981 kcal/mol@LB@Unfolding Energy - mRNA 3.3462 kcal/mol@LB@Unfolding Energy - sRNA 1.21803 kcal/mol@LB@@LB@Position - mRNA 22 -- 38@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 1 -- 7@LB@
63	0.0059	0.3087	b3834	ubiJ	-8.76	0.193647	289 -- 295	4 -- 10	aerobic ubiquinone synthesis protein SCP2 family protein	_____________288_____296\n_____________\|_______\|\n5'-GCU...CCGCU_______GCUGG-3'\n______________CGCGUCU\n______________\|\|\|\|\|\|\|\n______________GCGCAGA\n3'-UUU...UUUAC_______AAG-5'\n_____________\|_______\|\n_____________11______3\n	289 -- 295	4 -- 10	-11.2085 kcal/mol	1.2993 kcal/mol	1.14958 kcal/mol	288 296@LB@ \| \|@LB@5'-GCU...CCGCU GCUGG-3'@LB@ CGCGUCU@LB@ \|\|\|\|\|\|\|@LB@ GCGCAGA@LB@3'-UUU...UUUAC AAG-5'@LB@ \| \|@LB@ 11 3@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.2085 kcal/mol@LB@Unfolding Energy - mRNA 1.2993 kcal/mol@LB@Unfolding Energy - sRNA 1.14958 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 4 -- 10@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 4 -- 10@LB@
37	0.00241	0.2206	b2455	eutE	-11.61	0.064061	286 -- 298	3 -- 15	aldehyde oxidoreductase ethanolamine utilization protein	_____________285___________299\n_____________\|_____________\|\n5'-GGU...UCAUG_____G_______CG-3'\n______________AGAUG_GCGUUUU\n______________\|:\|\|\|_\|\|\|\|:\|\|\n______________UUUAC_CGCAGAA\n3'-UUU...UAUUG_____G_______AG-5'\n_____________\|_____________\|\n_____________16____________2\n	292 -- 298	3 -- 9	-14.5549 kcal/mol	1.73631 kcal/mol	1.20903 kcal/mol	285 299@LB@ \| \|@LB@5'-GGU...UCAUG G CG-3'@LB@ AGAUG GCGUUUU@LB@ \|:\|\|\| \|\|\|\|:\|\|@LB@ UUUAC CGCAGAA@LB@3'-UUU...UAUUG G AG-5'@LB@ \| \|@LB@ 16 2@LB@@LB@@LB@Energy -11.61 kcal/mol@LB@Hybridization Energy -14.5549 kcal/mol@LB@Unfolding Energy - mRNA 1.73631 kcal/mol@LB@Unfolding Energy - sRNA 1.20903 kcal/mol@LB@@LB@Position - mRNA 286 -- 298@LB@Position - sRNA 3 -- 15@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 3 -- 9@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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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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