Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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	Additional homologs
115	0.00375	0.1147	b1057	yceJ	-5.38	0.522888	37 -- 59	1 -- 23	putative cytochrome b561		_____________36_______________________60\n_____________\|________________________\|\n5'-UGA...CACCA_______C__AUG___A_______UAAAC...UGU-3'\n______________GACAUCU_UG___CUG_ACCC_AC\n______________:\|\|\|\|\|\|_\|:___\|\|\|_\|\|\|\|_\|\|\n______________UUGUAGA_AU___GAC_UGGG_UG\n3'-AUU...CUAUC__________GGA___A____A__-5'\n_____________\|_______________________\|\n_____________24______________________1\n	37 -- 43	17 -- 23	-17.2281 kcal/mol	3.85652 kcal/mol	8.01506 kcal/mol	36 60@LB@ \| \|@LB@5'-UGA...CACCA C AUG A UAAAC...UGU-3'@LB@ GACAUCU UG CUG ACCC AC@LB@ :\|\|\|\|\|\| \|: \|\|\| \|\|\|\| \|\|@LB@ UUGUAGA AU GAC UGGG UG@LB@3'-AUU...CUAUC GGA A A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -5.38 kcal/mol@LB@Hybridization Energy -17.2281 kcal/mol@LB@Unfolding Energy - mRNA 3.85652 kcal/mol@LB@Unfolding Energy - sRNA 8.01506 kcal/mol@LB@@LB@Position - mRNA 37 -- 59@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 17 -- 23@LB@
117	0.003878	0.1165	b3078	ygjI	-10.25	0.038289	174 -- 181	1 -- 8	putative transporter	b0899	_____________173______182\n_____________\|________\|\n5'-GGA...ACCGC________UCAUU...UUG-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	175 -- 181	1 -- 7	-12.7576 kcal/mol	0.416118 kcal/mol	2.11603 kcal/mol	173 182@LB@ \| \|@LB@5'-GGA...ACCGC UCAUU...UUG-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -12.7576 kcal/mol@LB@Unfolding Energy - mRNA 0.416118 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 174 -- 181@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 1 -- 7@LB@
118	0.003907	0.1165	b3827	yigM	-8.32	0.129405	260 -- 268	1 -- 9	putative inner membrane EamA-like transporter		_____________259_______269\n_____________\|_________\|\n5'-GGA...GGCGA_________GGGGC...UGG-3'\n______________GUACCUUGC\n______________\|\|\|\|\|:\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	262 -- 268	1 -- 7	-12.9582 kcal/mol	2.53078 kcal/mol	2.12872 kcal/mol	259 269@LB@ \| \|@LB@5'-GGA...GGCGA GGGGC...UGG-3'@LB@ GUACCUUGC@LB@ \|\|\|\|\|:\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.32 kcal/mol@LB@Hybridization Energy -12.9582 kcal/mol@LB@Unfolding Energy - mRNA 2.53078 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 260 -- 268@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 1 -- 7@LB@
119	0.003968	0.1172	b2765	queD	-8.07	0.149030	164 -- 172	1 -- 9	6-pyruvoyl tetrahydrobiopterin synthase (PTPS)		_____________163_______173\n_____________\|_________\|\n5'-AAC...UUCCG_________GGCGG...AUU-3'\n______________GUACUCUAC\n______________\|\|\|\|:\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	166 -- 172	1 -- 7	-12.1088 kcal/mol	1.92954 kcal/mol	2.12872 kcal/mol	163 173@LB@ \| \|@LB@5'-AAC...UUCCG GGCGG...AUU-3'@LB@ GUACUCUAC@LB@ \|\|\|\|:\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -12.1088 kcal/mol@LB@Unfolding Energy - mRNA 1.92954 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 164 -- 172@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 1 -- 7@LB@
126	0.00422	0.1178	b1621	malX	-14.96	0.000732	43 -- 87	1 -- 56	maltose and glucose-specific PTS enzyme IIB component and IIC component		_____________42__________________________________________________________88\n_____________\|___________________________________________________________\|\n5'-AUG...ACUCC____________C___________________A______________UAUU________ACCCG...GCA-3'\n______________CUGAUUAUGUGA_______________AGAUA_AACGUUUUACCUUU____UAUCUUAU\n______________\|:\|\|\|\|\|:\|\|\|\|_______________\|\|\|\|\|_\|\|\|:\|:\|\|\|\|\|\|:\|____\|\|:\|:\|\|:\n______________GGCUAAUGCACU_______________UCUAU_UUGUAGAAUGGAGA____AUGGGAUG\n3'-AUU...GUUUA____________UCAUUUUCCAGACUU_____C______________C___________-5'\n_____________\|__________________________________________________________\|\n_____________57_________________________________________________________1\n	81 -- 87	1 -- 7	-37.7188 kcal/mol	10.08 kcal/mol	12.7022 kcal/mol	42 88@LB@ \| \|@LB@5'-AUG...ACUCC C A UAUU ACCCG...GCA-3'@LB@ CUGAUUAUGUGA AGAUA AACGUUUUACCUUU UAUCUUAU@LB@ \|:\|\|\|\|\|:\|\|\|\| \|\|\|\|\| \|\|\|:\|:\|\|\|\|\|\|:\| \|\|:\|:\|\|:@LB@ GGCUAAUGCACU UCUAU UUGUAGAAUGGAGA AUGGGAUG@LB@3'-AUU...GUUUA UCAUUUUCCAGACUU C C -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -14.96 kcal/mol@LB@Hybridization Energy -37.7188 kcal/mol@LB@Unfolding Energy - mRNA 10.08 kcal/mol@LB@Unfolding Energy - sRNA 12.7022 kcal/mol@LB@@LB@Position - mRNA 43 -- 87@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 1 -- 7@LB@
129	0.004413	0.1199	b0062	araA	-8.60	0.109835	267 -- 273	1 -- 7	L-arabinose isomerase		_____________266_____274\n_____________\|_______\|\n5'-CGC...CGGAA_______GUCAG...ACG-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	267 -- 273	1 -- 7	-12.3746 kcal/mol	1.75625 kcal/mol	2.03949 kcal/mol	266 274@LB@ \| \|@LB@5'-CGC...CGGAA GUCAG...ACG-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.3746 kcal/mol@LB@Unfolding Energy - mRNA 1.75625 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 267 -- 273@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
132	0.004657	0.1239	b1200	dhaK	-7.52	0.201505	172 -- 179	1 -- 8	dihydroxyacetone kinase PTS-dependent dihydroxyacetone-binding subunit		_____________171______180\n_____________\|________\|\n5'-UUC...AUCCA________CGUAA...UGU-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	173 -- 179	1 -- 7	-12.1513 kcal/mol	2.5392 kcal/mol	2.11603 kcal/mol	171 180@LB@ \| \|@LB@5'-UUC...AUCCA CGUAA...UGU-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -12.1513 kcal/mol@LB@Unfolding Energy - mRNA 2.5392 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 172 -- 179@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
133	0.004686	0.1239	b3081	fadH	-11.00	0.022420	2 -- 21	1 -- 24	2 4-dienoyl-CoA reductase NADH and FMN-linked		_____________1________________________22\n_____________\|________________________\|\n__________5'-U_____C__________________AUGUG...ACC-3'\n______________GGACG_CUUAUC_C___GCCCUAC\n______________\|:\|\|:_\|\|\|\|:\|_\|___:\|\|\|\|\|\|\n______________CUUGU_GAAUGG_G___UGGGAUG\n3'-AUU...UCUAU_____A______A_ACA_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	15 -- 21	1 -- 7	-21.5738 kcal/mol	2.57038 kcal/mol	8.02158 kcal/mol	1 22@LB@ \| \|@LB@ 5'-U C AUGUG...ACC-3'@LB@ GGACG CUUAUC C GCCCUAC@LB@ \|:\|\|: \|\|\|\|:\| \| :\|\|\|\|\|\|@LB@ CUUGU GAAUGG G UGGGAUG@LB@3'-AUU...UCUAU A A ACA -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -21.5738 kcal/mol@LB@Unfolding Energy - mRNA 2.57038 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 2 -- 21@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 1 -- 7@LB@
134	0.004727	0.1241	b1655	mepH	-9.70	0.055155	231 -- 243	1 -- 13	murein DD-endopeptidase space-maker hydrolase		_____________230___________244\n_____________\|_____________\|\n5'-CGU...UCACG_____________UUUUU...AGA-3'\n______________CUCUGUGCUUUAC\n______________\|\|\|\|\|\|:\|::\|\|\|\n______________GAGACAUGGGAUG\n3'-AUU...GAAUG_____________-5'\n_____________\|____________\|\n_____________14___________1\n	237 -- 243	1 -- 7	-18.9465 kcal/mol	4.13106 kcal/mol	5.13393 kcal/mol	230 244@LB@ \| \|@LB@5'-CGU...UCACG UUUUU...AGA-3'@LB@ CUCUGUGCUUUAC@LB@ \|\|\|\|\|\|:\|::\|\|\|@LB@ GAGACAUGGGAUG@LB@3'-AUU...GAAUG -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -18.9465 kcal/mol@LB@Unfolding Energy - mRNA 4.13106 kcal/mol@LB@Unfolding Energy - sRNA 5.13393 kcal/mol@LB@@LB@Position - mRNA 231 -- 243@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 1 -- 7@LB@
139	0.005017	0.127	b2603	yfiR	-11.92	0.011246	223 -- 243	1 -- 19	putative periplasmic inhibitor of YfiN activity		_____________222___________________244\n_____________\|_____________________\|\n5'-GUA...ACUGU___________AUUC______UGACG...GUA-3'\n______________UCUUACUUCUG____UCCUGC\n______________\|\|\|\|\|\|:\|\|\|\|____:\|\|\|:\|\n______________AGAAUGGAGAC____GGGAUG\n3'-AUU...CUUGU___________AU________-5'\n_____________\|____________________\|\n_____________20___________________1\n	227 -- 233	9 -- 15	-21.8705 kcal/mol	2.00959 kcal/mol	7.96751 kcal/mol	222 244@LB@ \| \|@LB@5'-GUA...ACUGU AUUC UGACG...GUA-3'@LB@ UCUUACUUCUG UCCUGC@LB@ \|\|\|\|\|\|:\|\|\|\| :\|\|\|:\|@LB@ AGAAUGGAGAC GGGAUG@LB@3'-AUU...CUUGU AU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -21.8705 kcal/mol@LB@Unfolding Energy - mRNA 2.00959 kcal/mol@LB@Unfolding Energy - sRNA 7.96751 kcal/mol@LB@@LB@Position - mRNA 223 -- 243@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 9 -- 15@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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usability assessment

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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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