Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
64	0.003339	0.1645	b3166	truB	-7.27	0.093914	187 -- 199	36 -- 48	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase	_____________186___________200\n_____________\|_____________\|\n5'-GGC...ACGAC_________G___AAUGA...AAC-3'\n______________AGCAAGGAG_ACU\n______________\|\|\|\|\|\|:\|\|_\|\|\|\n______________UCGUUCUUC_UGA\n3'-UUU...CGAAU_________G___AUUUU...CAA-5'\n_____________\|_____________\|\n_____________49____________35\n	189 -- 195	40 -- 46	-16.8762 kcal/mol	3.76451 kcal/mol	5.83861 kcal/mol	186 200@LB@ \| \|@LB@5'-GGC...ACGAC G AAUGA...AAC-3'@LB@ AGCAAGGAG ACU@LB@ \|\|\|\|\|\|:\|\| \|\|\|@LB@ UCGUUCUUC UGA@LB@3'-UUU...CGAAU G AUUUU...CAA-5'@LB@ \| \|@LB@ 49 35@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -16.8762 kcal/mol@LB@Unfolding Energy - mRNA 3.76451 kcal/mol@LB@Unfolding Energy - sRNA 5.83861 kcal/mol@LB@@LB@Position - mRNA 187 -- 199@LB@Position - sRNA 36 -- 48@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 40 -- 46@LB@
179	0.02107	0.3768	b3226	nanR	-7.22	0.096643	281 -- 296	26 -- 41	sialic acid-inducible nan operon repressor	_____________280______________297\n_____________\|________________\|\n5'-AUU...CCGCU_____G_______C__UCCG-3'\n______________GGCGC_UAAAAAA_UC\n______________:\|\|:\|_\|\|\|\|\|\|\|_\|\|\n______________UCGUG_AUUUUUU_AG\n3'-UUU...GUUCU_____A_______A__CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	287 -- 293	29 -- 35	-11.6683 kcal/mol	2.7952 kcal/mol	1.64829 kcal/mol	280 297@LB@ \| \|@LB@5'-AUU...CCGCU G C UCCG-3'@LB@ GGCGC UAAAAAA UC@LB@ :\|\|:\| \|\|\|\|\|\|\| \|\|@LB@ UCGUG AUUUUUU AG@LB@3'-UUU...GUUCU A A CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -7.22 kcal/mol@LB@Hybridization Energy -11.6683 kcal/mol@LB@Unfolding Energy - mRNA 2.7952 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 29 -- 35@LB@
24	0.000694	0.09021	b2531	iscR	-7.21	0.097486	53 -- 65	27 -- 41	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________52______________66\n_____________\|_______________\|\n5'-AUG...AAAAU_______________AAAUA...AAC-3'\n______________GGCACU__GAAGGUU\n______________:\|\|\|\|\|__:\|\|::\|\|\n______________UCGUGA__UUUUUAA\n3'-UUU...GUUCU______AU_______GCAAU...CAA-5'\n_____________\|_______________\|\n_____________42______________26\n	59 -- 65	27 -- 33	-10.1429 kcal/mol	1.29 kcal/mol	1.6427 kcal/mol	52 66@LB@ \| \|@LB@5'-AUG...AAAAU AAAUA...AAC-3'@LB@ GGCACU GAAGGUU@LB@ :\|\|\|\|\| :\|\|::\|\|@LB@ UCGUGA UUUUUAA@LB@3'-UUU...GUUCU AU GCAAU...CAA-5'@LB@ \| \|@LB@ 42 26@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -10.1429 kcal/mol@LB@Unfolding Energy - mRNA 1.29 kcal/mol@LB@Unfolding Energy - sRNA 1.6427 kcal/mol@LB@@LB@Position - mRNA 53 -- 65@LB@Position - sRNA 27 -- 41@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 27 -- 33@LB@
43	0.001794	0.1344	b0631	ybeD	-7.18	0.099343	171 -- 193	16 -- 40	UPF0250 family protein	_____________170________________________194\n_____________\|__________________________\|\n5'-GCU...GAGUU__U______UUA______________AGCUG...AAG-3'\n______________GC_AUUUAA______CGUUACGCCGG\n______________\|\|_\|:\|\|\|\|______\|\|\|\|\|\|:\|\|:\|\n______________CG_UGAAUU______GCAAUGUGGUC\n3'-UUU...UUCUU_________UUUUAA___________CUUUA...CAA-5'\n_____________\|__________________________\|\n_____________41_________________________15\n	187 -- 193	16 -- 22	-19.4847 kcal/mol	3.10673 kcal/mol	9.1996 kcal/mol	170 194@LB@ \| \|@LB@5'-GCU...GAGUU U UUA AGCUG...AAG-3'@LB@ GC AUUUAA CGUUACGCCGG@LB@ \|\| \|:\|\|\|\| \|\|\|\|\|\|:\|\|:\|@LB@ CG UGAAUU GCAAUGUGGUC@LB@3'-UUU...UUCUU UUUUAA CUUUA...CAA-5'@LB@ \| \|@LB@ 41 15@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -19.4847 kcal/mol@LB@Unfolding Energy - mRNA 3.10673 kcal/mol@LB@Unfolding Energy - sRNA 9.1996 kcal/mol@LB@@LB@Position - mRNA 171 -- 193@LB@Position - sRNA 16 -- 40@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 16 -- 22@LB@
105	0.008762	0.2688	b2735	ygbI	-7.10	0.103888	185 -- 196	38 -- 49	DeoR family putative transcriptional regulator	_____________184__________197\n_____________\|____________\|\n5'-UUC...GGACA___G________AAAGU...AUA-3'\n______________AAG_AAGGAGCA\n______________\|\|\|_\|\|\|:\|\|\|\|\n______________UUC_UUCUUCGU\n3'-UUU...ACGAA___G________GAAUU...CAA-5'\n_____________\|____________\|\n_____________50___________37\n	190 -- 196	38 -- 44	-14.2659 kcal/mol	1.1364 kcal/mol	6.02696 kcal/mol	184 197@LB@ \| \|@LB@5'-UUC...GGACA G AAAGU...AUA-3'@LB@ AAG AAGGAGCA@LB@ \|\|\| \|\|\|:\|\|\|\|@LB@ UUC UUCUUCGU@LB@3'-UUU...ACGAA G GAAUU...CAA-5'@LB@ \| \|@LB@ 50 37@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -14.2659 kcal/mol@LB@Unfolding Energy - mRNA 1.1364 kcal/mol@LB@Unfolding Energy - sRNA 6.02696 kcal/mol@LB@@LB@Position - mRNA 185 -- 196@LB@Position - sRNA 38 -- 49@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 38 -- 44@LB@
137	0.01315	0.3087	b2239	glpQ	-7.04	0.107729	242 -- 248	36 -- 42	periplasmic glycerophosphodiester phosphodiesterase	_____________241_____249\n_____________\|_______\|\n5'-CGG...AUGAU_______AUAGU...UCA-3'\n______________GAGCACU\n______________:\|\|\|\|\|\|\n______________UUCGUGA\n3'-UUU...CGUUC_______AUUUU...CAA-5'\n_____________\|_______\|\n_____________43______35\n	242 -- 248	36 -- 42	-9.09813 kcal/mol	0.455964 kcal/mol	1.60154 kcal/mol	241 249@LB@ \| \|@LB@5'-CGG...AUGAU AUAGU...UCA-3'@LB@ GAGCACU@LB@ :\|\|\|\|\|\|@LB@ UUCGUGA@LB@3'-UUU...CGUUC AUUUU...CAA-5'@LB@ \| \|@LB@ 43 35@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -9.09813 kcal/mol@LB@Unfolding Energy - mRNA 0.455964 kcal/mol@LB@Unfolding Energy - sRNA 1.60154 kcal/mol@LB@@LB@Position - mRNA 242 -- 248@LB@Position - sRNA 36 -- 42@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 36 -- 42@LB@
15	0.0003116	0.06692	b2149	mglA	-7.01	0.109495	281 -- 289	33 -- 41	methyl-galactoside ABC transporter ATPase	_____________280_______290\n_____________\|_________\|\n5'-CGA...GUUAA_________UAACG...AUU-3'\n______________GGCACUUGA\n______________:\|\|\|\|\|\|:\|\n______________UCGUGAAUU\n3'-UUU...GUUCU_________UUUUA...CAA-5'\n_____________\|_________\|\n_____________42________32\n	283 -- 289	33 -- 39	-11.227 kcal/mol	2.59529 kcal/mol	1.6188 kcal/mol	280 290@LB@ \| \|@LB@5'-CGA...GUUAA UAACG...AUU-3'@LB@ GGCACUUGA@LB@ :\|\|\|\|\|\|:\|@LB@ UCGUGAAUU@LB@3'-UUU...GUUCU UUUUA...CAA-5'@LB@ \| \|@LB@ 42 32@LB@@LB@@LB@Energy -7.01 kcal/mol@LB@Hybridization Energy -11.227 kcal/mol@LB@Unfolding Energy - mRNA 2.59529 kcal/mol@LB@Unfolding Energy - sRNA 1.6188 kcal/mol@LB@@LB@Position - mRNA 281 -- 289@LB@Position - sRNA 33 -- 41@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 33 -- 39@LB@
47	0.002119	0.1452	b0694	kdpE	-6.96	0.113004	177 -- 189	26 -- 38	response regulator in two-component regulatory system with KdpD	_____________176___________190\n_____________\|_____________\|\n5'-ACG...CCUGA_____________CAUGA...CGC-3'\n______________ACUUGAAGAAUUU\n______________\|\|\|\|:\|\|:\|\|\|\|:\n______________UGAAUUUUUUAAG\n3'-UUU...CUUCG_____________CAAUG...CAA-5'\n_____________\|_____________\|\n_____________39____________25\n	179 -- 185	30 -- 36	-10.6038 kcal/mol	2.21135 kcal/mol	1.43364 kcal/mol	176 190@LB@ \| \|@LB@5'-ACG...CCUGA CAUGA...CGC-3'@LB@ ACUUGAAGAAUUU@LB@ \|\|\|\|:\|\|:\|\|\|\|:@LB@ UGAAUUUUUUAAG@LB@3'-UUU...CUUCG CAAUG...CAA-5'@LB@ \| \|@LB@ 39 25@LB@@LB@@LB@Energy -6.96 kcal/mol@LB@Hybridization Energy -10.6038 kcal/mol@LB@Unfolding Energy - mRNA 2.21135 kcal/mol@LB@Unfolding Energy - sRNA 1.43364 kcal/mol@LB@@LB@Position - mRNA 177 -- 189@LB@Position - sRNA 26 -- 38@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 30 -- 36@LB@
190	0.02239	0.3796	b0724	sdhB	-6.89	0.117799	143 -- 176	24 -- 60	succinate dehydrogenase FeS subunit	_____________142____________________________________177\n_____________\|______________________________________\|\n5'-UUU...GAACC_________GCCC____UUCC____C____________ACUUA...UGA-3'\n______________GAAAC_UGC____GGCA_____CGC___GAAGAUUCGU\n______________\|\|\|\|\|_\|\|\|____:\|\|\|_____\|:\|___:\|\|:\|\|\|\|\|\|\n______________CUUUG_ACG____UCGU_____GUG___UUUUUAAGCA\n3'-UUU...CCCUA_____A___AAU_____UCUUC___AAU__________AUGUG...CAA-5'\n_____________\|______________________________________\|\n_____________61_____________________________________23\n	170 -- 176	24 -- 30	-22.9017 kcal/mol	9.73835 kcal/mol	6.27609 kcal/mol	142 177@LB@ \| \|@LB@5'-UUU...GAACC GCCC UUCC C ACUUA...UGA-3'@LB@ GAAAC UGC GGCA CGC GAAGAUUCGU@LB@ \|\|\|\|\| \|\|\| :\|\|\| \|:\| :\|\|:\|\|\|\|\|\|@LB@ CUUUG ACG UCGU GUG UUUUUAAGCA@LB@3'-UUU...CCCUA A AAU UCUUC AAU AUGUG...CAA-5'@LB@ \| \|@LB@ 61 23@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -22.9017 kcal/mol@LB@Unfolding Energy - mRNA 9.73835 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 143 -- 176@LB@Position - sRNA 24 -- 60@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 24 -- 30@LB@
177	0.02045	0.3721	b3148	yraN	-6.85	0.120614	263 -- 276	37 -- 54	UPF0102 family protein	_____________262________________277\n_____________\|__________________\|\n5'-GGU...GGCGA__________________AAGCG...GCA-3'\n______________UGC____GUGGGAAGCAC\n______________\|\|\|____\|:::\|\|\|\|\|\|\|\n______________ACG____CGUUCUUCGUG\n3'-UUU...UUUGA___AAUU___________AAUUU...CAA-5'\n_____________\|__________________\|\n_____________55_________________36\n	270 -- 276	37 -- 43	-17.1481 kcal/mol	4.14332 kcal/mol	6.1584 kcal/mol	262 277@LB@ \| \|@LB@5'-GGU...GGCGA AAGCG...GCA-3'@LB@ UGC GUGGGAAGCAC@LB@ \|\|\| \|:::\|\|\|\|\|\|\|@LB@ ACG CGUUCUUCGUG@LB@3'-UUU...UUUGA AAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 55 36@LB@@LB@@LB@Energy -6.85 kcal/mol@LB@Hybridization Energy -17.1481 kcal/mol@LB@Unfolding Energy - mRNA 4.14332 kcal/mol@LB@Unfolding Energy - sRNA 6.1584 kcal/mol@LB@@LB@Position - mRNA 263 -- 276@LB@Position - sRNA 37 -- 54@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 37 -- 43@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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