Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
112	0.01793	0.5155	b1418	cybB	-10.08	0.093429	125 -- 145	33 -- 57	cytochrome b561	_____________124_______________________146\n_____________\|_________________________\|\n5'-AAC...AAAAC_________________________AUUUU...UCC-3'\n______________GGGUGAACA_AUAUUU___AAUGAA\n______________\|\|\|\|:\|\|\|\|_\|:\|\|\|:___\|\|\|\|\|\|\n______________CCCAUUUGU_UGUAAG___UUACUU\n3'-UUU...UUAUC_________C______UCU______ACUGC...UCG-5'\n_____________\|_________________________\|\n_____________58________________________32\n	127 -- 133	49 -- 55	-19.5073 kcal/mol	3.1607 kcal/mol	6.2643 kcal/mol	124 146@LB@ \| \|@LB@5'-AAC...AAAAC AUUUU...UCC-3'@LB@ GGGUGAACA AUAUUU AAUGAA@LB@ \|\|\|\|:\|\|\|\| \|:\|\|\|: \|\|\|\|\|\|@LB@ CCCAUUUGU UGUAAG UUACUU@LB@3'-UUU...UUAUC C UCU ACUGC...UCG-5'@LB@ \| \|@LB@ 58 32@LB@@LB@@LB@Energy -10.08 kcal/mol@LB@Hybridization Energy -19.5073 kcal/mol@LB@Unfolding Energy - mRNA 3.1607 kcal/mol@LB@Unfolding Energy - sRNA 6.2643 kcal/mol@LB@@LB@Position - mRNA 125 -- 145@LB@Position - sRNA 33 -- 57@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 49 -- 55@LB@
110	0.01732	0.5155	b1800	dmlA	-11.31	0.051964	127 -- 183	1 -- 58	D-malate oxidase NAD-dependent; putative tartrate dehydrogenase	_____________126___________________________________________________________184\n_____________\|_____________________________________________________________\|\n5'-GGU...GUUAC____AUU___UCCUU_____UCAAUUAUAG__________UU______C___UU_______CAGGA...GCU-3'\n______________GGGG___AAU_____UUCAG__________GAUGGUGAUG______GU_AAU__UGAUGGU\n______________\|\|\|\|___\|\|:_____\|\|\|\|\|__________\|\|:\|\|\|:\|\|:______\|\|_\|\|\|__\|\|\|\|:\|:\n______________CCCC___UUG_____AAGUC__________CUGCCAUUAU______CA_UUA__ACUAUCG\n3'-UUU...UUUAU____AU____UCUGU_____UUUACUUA____________UUAUUU__A___CU_______-5'\n_____________\|____________________________________________________________\|\n_____________59___________________________________________________________1\n	177 -- 183	1 -- 7	-30.6237 kcal/mol	12.9772 kcal/mol	6.33758 kcal/mol	126 184@LB@ \| \|@LB@5'-GGU...GUUAC AUU UCCUU UCAAUUAUAG UU C UU CAGGA...GCU-3'@LB@ GGGG AAU UUCAG GAUGGUGAUG GU AAU UGAUGGU@LB@ \|\|\|\| \|\|: \|\|\|\|\| \|\|:\|\|\|:\|\|: \|\| \|\|\| \|\|\|\|:\|:@LB@ CCCC UUG AAGUC CUGCCAUUAU CA UUA ACUAUCG@LB@3'-UUU...UUUAU AU UCUGU UUUACUUA UUAUUU A CU -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -11.31 kcal/mol@LB@Hybridization Energy -30.6237 kcal/mol@LB@Unfolding Energy - mRNA 12.9772 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 127 -- 183@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 1 -- 7@LB@
156	0.02543	0.526	b2805	fucR	-9.08	0.146396	128 -- 135	52 -- 59	l-fucose operon activator	_____________127______136\n_____________\|________\|\n5'-CAC...AAAAA________CACCG...AAA-3'\n______________AGGGGUAA\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAUU\n3'-UUU...CUUUA________UGUCU...UCG-5'\n_____________\|________\|\n_____________60_______51\n	129 -- 135	52 -- 58	-12.2757 kcal/mol	3.13783 kcal/mol	0.0599826 kcal/mol	127 136@LB@ \| \|@LB@5'-CAC...AAAAA CACCG...AAA-3'@LB@ AGGGGUAA@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAUU@LB@3'-UUU...CUUUA UGUCU...UCG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -12.2757 kcal/mol@LB@Unfolding Energy - mRNA 3.13783 kcal/mol@LB@Unfolding Energy - sRNA 0.0599826 kcal/mol@LB@@LB@Position - mRNA 128 -- 135@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 52 -- 58@LB@
135	0.02191	0.526	b1342	ydaN	-17.19	0.001818	129 -- 197	1 -- 58	putative Zn(II) transporter	_____________128______________________________________________________________________198\n_____________\|________________________________________________________________________\|\n5'-CGU...GUAAU_______UG_______GCGUAACAGGGC______GCUA____UACA________UGC___________A___ACUGU...AUG-3'\n______________GGGGUGA__AGAUGUU____________CAGAAG_____GAC______AAAUAA___GUUGAUGAUGG_GGC\n______________\|\|\|\|\|:\|__\|\|\|::\|\|____________\|\|\|\|\|:_____\|\|\|______\|\|\|\|\|\|___\|\|\|:\|\|\|\|\|\|:_:\|\|\n______________CCCCAUU__UCUGUAA____________GUCUUU_____CUG______UUUAUU___CAAUUACUACU_UCG\n3'-UUU...UUUAU_______UG_________________________ACUUA___CCAUUA______U_____________A___-5'\n_____________\|_______________________________________________________________________\|\n_____________59______________________________________________________________________1\n	187 -- 193	5 -- 11	-40.4273 kcal/mol	16.9018 kcal/mol	6.33758 kcal/mol	128 198@LB@ \| \|@LB@5'-CGU...GUAAU UG GCGUAACAGGGC GCUA UACA UGC A ACUGU...AUG-3'@LB@ GGGGUGA AGAUGUU CAGAAG GAC AAAUAA GUUGAUGAUGG GGC@LB@ \|\|\|\|\|:\| \|\|\|::\|\| \|\|\|\|\|: \|\|\| \|\|\|\|\|\| \|\|\|:\|\|\|\|\|\|: :\|\|@LB@ CCCCAUU UCUGUAA GUCUUU CUG UUUAUU CAAUUACUACU UCG@LB@3'-UUU...UUUAU UG ACUUA CCAUUA U A -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -17.19 kcal/mol@LB@Hybridization Energy -40.4273 kcal/mol@LB@Unfolding Energy - mRNA 16.9018 kcal/mol@LB@Unfolding Energy - sRNA 6.33758 kcal/mol@LB@@LB@Position - mRNA 129 -- 197@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 5 -- 11@LB@
40	0.004127	0.3349	b1659	ydhB	-12.78	0.024485	130 -- 177	1 -- 61	LysR family putative transcriptional regulator	_____________129_______________________________________________________________178\n_____________\|_________________________________________________________________\|\n5'-CGA...AAAGU______A_____AU_____________________________UU_______________C____UUCAA...UCA-3'\n______________GUAGGG_GUGAA__UAG_UGUU_____GUGAA__ACGGUAAUA___________UGAUGA_UGGU\n______________:\|\|\|\|\|_\|\|:\|\|__:\|\|_::\|\|_____:\|\|\|\|__\|\|\|\|\|\|\|\|\|___________\|\|\|\|\|\|_\|:\|:\n______________UAUCCC_CAUUU__GUC_GUAA_____UACUU__UGCCAUUAU___________ACUACU_AUCG\n3'-UUU...AACUU_________________U____GUCUU_____AC_________UUAUUUCAAUU___________-5'\n_____________\|________________________________________________________________\|\n_____________62_______________________________________________________________1\n	158 -- 164	22 -- 28	-31.01 kcal/mol	11.8895 kcal/mol	6.344 kcal/mol	129 178@LB@ \| \|@LB@5'-CGA...AAAGU A AU UU C UUCAA...UCA-3'@LB@ GUAGGG GUGAA UAG UGUU GUGAA ACGGUAAUA UGAUGA UGGU@LB@ :\|\|\|\|\| \|\|:\|\| :\|\| ::\|\| :\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\|:@LB@ UAUCCC CAUUU GUC GUAA UACUU UGCCAUUAU ACUACU AUCG@LB@3'-UUU...AACUU U GUCUU AC UUAUUUCAAUU -5'@LB@ \| \|@LB@ 62 1@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -31.01 kcal/mol@LB@Unfolding Energy - mRNA 11.8895 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 130 -- 177@LB@Position - sRNA 1 -- 61@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 22 -- 28@LB@
50	0.005695	0.3739	b1086	rluC	-13.13	0.020232	139 -- 168	28 -- 55	23S rRNA pseudouridine(955 2504 2580) synthase	_____________138____________________________169\n_____________\|______________________________\|\n5'-UCC...CAAAA_______UAA____AG_A____________CGAAU...UAC-3'\n______________GUAAAUA___GCAU__A_AAAUGAGUGGCG\n______________\|\|\|\|\|:\|___:\|\|\|__\|_\|\|\|\|\|\|:\|\|:\|\|\n______________CAUUUGU___UGUA__U_UUUACUUACUGC\n3'-UUU...AUCCC_______C______AG_C____________CAUUA...UCG-5'\n_____________\|______________________________\|\n_____________56_____________________________27\n	161 -- 167	29 -- 35	-21.8911 kcal/mol	2.47099 kcal/mol	6.28725 kcal/mol	138 169@LB@ \| \|@LB@5'-UCC...CAAAA UAA AG A CGAAU...UAC-3'@LB@ GUAAAUA GCAU A AAAUGAGUGGCG@LB@ \|\|\|\|\|:\| :\|\|\| \| \|\|\|\|\|\|:\|\|:\|\|@LB@ CAUUUGU UGUA U UUUACUUACUGC@LB@3'-UUU...AUCCC C AG C CAUUA...UCG-5'@LB@ \| \|@LB@ 56 27@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -21.8911 kcal/mol@LB@Unfolding Energy - mRNA 2.47099 kcal/mol@LB@Unfolding Energy - sRNA 6.28725 kcal/mol@LB@@LB@Position - mRNA 139 -- 168@LB@Position - sRNA 28 -- 55@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 29 -- 35@LB@
174	0.02825	0.531	b2154	yeiG	-9.96	0.098977	140 -- 169	15 -- 51	S-formylglutathione hydrolase	_____________139_____________________________________170\n_____________\|_______________________________________\|\n5'-GCU...UACUC____C________________AA______U_________AAAUU...UUC-3'\n______________ACAG_ACAU_______UGAAU__ACGGUA___GAUGAAG\n______________\|\|\|\|_\|\|\|\|_______\|\|\|\|\|__\|\|\|\|\|\|___:\|\|:\|\|\|\n______________UGUC_UGUA_______ACUUA__UGCCAU___UUAUUUC\n3'-UUU...CCAUU_________AGUCUUU_____C_______UAU_______AAUUA...UCG-5'\n_____________\|_______________________________________\|\n_____________52______________________________________14\n	163 -- 169	15 -- 21	-20.0225 kcal/mol	3.74261 kcal/mol	6.32297 kcal/mol	139 170@LB@ \| \|@LB@5'-GCU...UACUC C AA U AAAUU...UUC-3'@LB@ ACAG ACAU UGAAU ACGGUA GAUGAAG@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\| \|\|\|\|\|\| :\|\|:\|\|\|@LB@ UGUC UGUA ACUUA UGCCAU UUAUUUC@LB@3'-UUU...CCAUU AGUCUUU C UAU AAUUA...UCG-5'@LB@ \| \|@LB@ 52 14@LB@@LB@@LB@Energy -9.96 kcal/mol@LB@Hybridization Energy -20.0225 kcal/mol@LB@Unfolding Energy - mRNA 3.74261 kcal/mol@LB@Unfolding Energy - sRNA 6.32297 kcal/mol@LB@@LB@Position - mRNA 140 -- 169@LB@Position - sRNA 15 -- 51@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 15 -- 21@LB@
108	0.01698	0.5123	b0078	ilvH	-10.97	0.061484	141 -- 180	1 -- 51	acetolactate synthase 3 small subunit valine-sensitive	_____________140_________________________________________________181\n_____________\|___________________________________________________\|\n5'-GCC...CCGAU______UCG___________________________AU_______UA____AAAAC...UGA-3'\n______________GCAGAU___CGGG_______GGCGG_AAUGGAUGAA____GUGGU___AGC\n______________:\|\|\|\|:___\|:\|:_______\|:\|\|\|_\|\|\|::\|\|:\|\|____:\|\|:\|___\|\|\|\n______________UGUCUG___GUCU_______CUGCC_UUAUUUAUUU____UACUA___UCG\n3'-UUU...CCAUU______UAA____UUACUUA_____A__________CAAU_____CUA___-5'\n_____________\|__________________________________________________\|\n_____________52_________________________________________________1\n	162 -- 168	16 -- 22	-27.7823 kcal/mol	10.4814 kcal/mol	6.33528 kcal/mol	140 181@LB@ \| \|@LB@5'-GCC...CCGAU UCG AU UA AAAAC...UGA-3'@LB@ GCAGAU CGGG GGCGG AAUGGAUGAA GUGGU AGC@LB@ :\|\|\|\|: \|:\|: \|:\|\|\| \|\|\|::\|\|:\|\| :\|\|:\| \|\|\|@LB@ UGUCUG GUCU CUGCC UUAUUUAUUU UACUA UCG@LB@3'-UUU...CCAUU UAA UUACUUA A CAAU CUA -5'@LB@ \| \|@LB@ 52 1@LB@@LB@@LB@Energy -10.97 kcal/mol@LB@Hybridization Energy -27.7823 kcal/mol@LB@Unfolding Energy - mRNA 10.4814 kcal/mol@LB@Unfolding Energy - sRNA 6.33528 kcal/mol@LB@@LB@Position - mRNA 141 -- 180@LB@Position - sRNA 1 -- 51@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 16 -- 22@LB@
69	0.009861	0.4523	b0879	macB	-12.35	0.030572	144 -- 182	1 -- 59	macrolide ABC transporter peremase/ATPase	_____________143___________________________________________________________183\n_____________\|_____________________________________________________________\|\n5'-AAU...GUCAA____CUUG_____________________________________________________CAAAC...CGG-3'\n______________AGGG____AAGCGGGC_______GAUGAA_G_UGGUGAU____________UGGUGA_GGC\n______________\|\|\|\|____\|\|:\|:\|:\|_______:\|\|\|\|\|_\|_:\|\|\|:\|\|____________\|\|:\|\|\|_:\|\|\n______________UCCC____UUUGUCUG_______UUACUU_C_GCCAUUA____________ACUACU_UCG\n3'-UUU...CUUUA____CA__________UAAGUCU______A_U_______UUUAUUUCAAUU______A___-5'\n_____________\|____________________________________________________________\|\n_____________60___________________________________________________________1\n	167 -- 173	23 -- 29	-29.0987 kcal/mol	10.4067 kcal/mol	6.33764 kcal/mol	143 183@LB@ \| \|@LB@5'-AAU...GUCAA CUUG CAAAC...CGG-3'@LB@ AGGG AAGCGGGC GAUGAA G UGGUGAU UGGUGA GGC@LB@ \|\|\|\| \|\|:\|:\|:\| :\|\|\|\|\| \| :\|\|\|:\|\| \|\|:\|\|\| :\|\|@LB@ UCCC UUUGUCUG UUACUU C GCCAUUA ACUACU UCG@LB@3'-UUU...CUUUA CA UAAGUCU A U UUUAUUUCAAUU A -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -12.35 kcal/mol@LB@Hybridization Energy -29.0987 kcal/mol@LB@Unfolding Energy - mRNA 10.4067 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 144 -- 182@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 23 -- 29@LB@
182	0.03007	0.5424	b3131	agaR	-10.52	0.076061	148 -- 177	28 -- 59	transcriptional repressor of the aga regulon	_____________147______________________________178\n_____________\|________________________________\|\n5'-CAG...UAGAA___C__U________AAAC_____________AAAGU...AGG-3'\n______________AGG_GU_AAUAGGCA____GAAAUGAA__ACG\n______________\|\|\|_\|\|_\|\|:\|\|:\|\|____\|\|\|\|\|\|\|\|__\|\|\|\n______________UCC_CA_UUGUCUGU____CUUUACUU__UGC\n3'-UUU...CUUUA___C__U________AAGU________AC___CAUUA...UCG-5'\n_____________\|________________________________\|\n_____________60_______________________________27\n	167 -- 173	34 -- 40	-23.0737 kcal/mol	6.26419 kcal/mol	6.28754 kcal/mol	147 178@LB@ \| \|@LB@5'-CAG...UAGAA C U AAAC AAAGU...AGG-3'@LB@ AGG GU AAUAGGCA GAAAUGAA ACG@LB@ \|\|\| \|\| \|\|:\|\|:\|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ UCC CA UUGUCUGU CUUUACUU UGC@LB@3'-UUU...CUUUA C U AAGU AC CAUUA...UCG-5'@LB@ \| \|@LB@ 60 27@LB@@LB@@LB@Energy -10.52 kcal/mol@LB@Hybridization Energy -23.0737 kcal/mol@LB@Unfolding Energy - mRNA 6.26419 kcal/mol@LB@Unfolding Energy - sRNA 6.28754 kcal/mol@LB@@LB@Position - mRNA 148 -- 177@LB@Position - sRNA 28 -- 59@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 34 -- 40@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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