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
101	0.01678	0.5385	b0452	tesB	-11.66	0.054224	159 -- 170	73 -- 84	acyl-CoA thioesterase 2	_____________158__________171\n_____________\|____________\|\n5'-CAA...UCAAC____U_______GCUGC...AGG-3'\n______________UCAC_UUGGCUU\n______________\|\|\|\|_\|\|\|\|\|\|\|\n______________AGUG_AACCGAA\n3'-CGC...UUUCA____C_______AUCAA...AAG-5'\n_____________\|____________\|\n_____________85___________72\n	164 -- 170	73 -- 79	-14.9501 kcal/mol	2.7795 kcal/mol	0.508835 kcal/mol	158 171@LB@ \| \|@LB@5'-CAA...UCAAC U GCUGC...AGG-3'@LB@ UCAC UUGGCUU@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ AGUG AACCGAA@LB@3'-CGC...UUUCA C AUCAA...AAG-5'@LB@ \| \|@LB@ 85 72@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -14.9501 kcal/mol@LB@Unfolding Energy - mRNA 2.7795 kcal/mol@LB@Unfolding Energy - sRNA 0.508835 kcal/mol@LB@@LB@Position - mRNA 159 -- 170@LB@Position - sRNA 73 -- 84@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 73 -- 79@LB@
102	0.01732	0.5385	b3442	yhhZ	-11.63	0.054951	288 -- 294	75 -- 81	putative Hcp1 family polymorphic toxin protein; putative colicin-like DNase/tRNase activity	_____________287_____295\n_____________\|_______\|\n5'-AUU...GUAAU_______AGAGCG-3'\n______________CGUUGGC\n______________\|\|\|\|\|\|\|\n______________GCAACCG\n3'-CGC...CAAGU_______AAAUC...AAG-5'\n_____________\|_______\|\n_____________82______74\n	288 -- 294	75 -- 81	-12.2648 kcal/mol	0.311297 kcal/mol	0.324493 kcal/mol	287 295@LB@ \| \|@LB@5'-AUU...GUAAU AGAGCG-3'@LB@ CGUUGGC@LB@ \|\|\|\|\|\|\|@LB@ GCAACCG@LB@3'-CGC...CAAGU AAAUC...AAG-5'@LB@ \| \|@LB@ 82 74@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -12.2648 kcal/mol@LB@Unfolding Energy - mRNA 0.311297 kcal/mol@LB@Unfolding Energy - sRNA 0.324493 kcal/mol@LB@@LB@Position - mRNA 288 -- 294@LB@Position - sRNA 75 -- 81@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 75 -- 81@LB@
103	0.01739	0.5385	b0945	pyrD	-8.62	0.180746	193 -- 204	79 -- 90	dihydro-orotate oxidase FMN-linked	_____________192__________205\n_____________\|____________\|\n5'-UGU...UCCAG____________ACUAC...CGU-3'\n______________GAGAGUUCAUGU\n______________:\|:\|\|\|\|\|\|:\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	198 -- 204	79 -- 85	-13.8118 kcal/mol	4.6828 kcal/mol	0.506924 kcal/mol	192 205@LB@ \| \|@LB@5'-UGU...UCCAG ACUAC...CGU-3'@LB@ GAGAGUUCAUGU@LB@ :\|:\|\|\|\|\|\|:\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -13.8118 kcal/mol@LB@Unfolding Energy - mRNA 4.6828 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 193 -- 204@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 79 -- 85@LB@
104	0.0176	0.5385	b2788	gudX	-9.05	0.153387	171 -- 179	57 -- 65	glucarate dehydratase-related protein substrate unknown	_____________170_______180\n_____________\|_________\|\n5'-CGG...GCGUA_________AACCU...CAU-3'\n______________UCGAGUUGA\n______________\|\|\|\|\|\|\|\|\|\n______________AGCUCAACU\n3'-CGC...CAAUA_________CUUUG...AAG-5'\n_____________\|_________\|\n_____________66________56\n	173 -- 179	57 -- 63	-12.8916 kcal/mol	2.7095 kcal/mol	1.13183 kcal/mol	170 180@LB@ \| \|@LB@5'-CGG...GCGUA AACCU...CAU-3'@LB@ UCGAGUUGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ AGCUCAACU@LB@3'-CGC...CAAUA CUUUG...AAG-5'@LB@ \| \|@LB@ 66 56@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -12.8916 kcal/mol@LB@Unfolding Energy - mRNA 2.7095 kcal/mol@LB@Unfolding Energy - sRNA 1.13183 kcal/mol@LB@@LB@Position - mRNA 171 -- 179@LB@Position - sRNA 57 -- 65@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 57 -- 63@LB@
105	0.01788	0.5385	b0619	citA	-6.78	0.351941	4 -- 24	64 -- 89	sensory histidine kinase in two-component regulatory system with CitB	_____________3__________________________25\n_____________\|__________________________\|\n________5'-CAU______AG__________________AUUUA...UCA-3'\n______________AGAGUU_____UGGUUUU__UUAUUU\n______________\|:\|\|\|\|_____\|\|\|:\|\|\|__\|\|\|\|\|:\n______________UUUCAA_____ACCGAAA__AAUAAG\n3'-CGC...GGCGU______GUGCA_______UC______CUCAA...AAG-5'\n_____________\|__________________________\|\n_____________90_________________________63\n	12 -- 18	72 -- 78	-10.9037 kcal/mol	3.54899 kcal/mol	0.576654 kcal/mol	3 25@LB@ \| \|@LB@ 5'-CAU AG AUUUA...UCA-3'@LB@ AGAGUU UGGUUUU UUAUUU@LB@ \|:\|\|\|\| \|\|\|:\|\|\| \|\|\|\|\|:@LB@ UUUCAA ACCGAAA AAUAAG@LB@3'-CGC...GGCGU GUGCA UC CUCAA...AAG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -10.9037 kcal/mol@LB@Unfolding Energy - mRNA 3.54899 kcal/mol@LB@Unfolding Energy - sRNA 0.576654 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 12 -- 18@LB@Position Seed - sRNA 72 -- 78@LB@
106	0.01861	0.5385	b2754	ygbF	-9.88	0.110684	283 -- 300	13 -- 30	CRISPR adaptation ssRNA endonuclease	_____________282_______________300\n_____________\|_________________\|\n5'-UGG...ACGUG_______AUAUGU_____-3'\n______________CAGGGGU______AGGUG\n______________\|\|:\|\|\|\|______\|\|\|\|\|\n______________GUUCCCA______UCCAC\n3'-CGC...CUGAA_______AUUUUC_____GGCGA...AAG-5'\n_____________\|__________________\|\n_____________31_________________12\n	283 -- 289	24 -- 30	-16.4011 kcal/mol	3.18452 kcal/mol	3.3319 kcal/mol	282 300@LB@ \| \|@LB@5'-UGG...ACGUG AUAUGU -3'@LB@ CAGGGGU AGGUG@LB@ \|\|:\|\|\|\| \|\|\|\|\|@LB@ GUUCCCA UCCAC@LB@3'-CGC...CUGAA AUUUUC GGCGA...AAG-5'@LB@ \| \|@LB@ 31 12@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -16.4011 kcal/mol@LB@Unfolding Energy - mRNA 3.18452 kcal/mol@LB@Unfolding Energy - sRNA 3.3319 kcal/mol@LB@@LB@Position - mRNA 283 -- 300@LB@Position - sRNA 13 -- 30@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 24 -- 30@LB@
107	0.01867	0.5385	b1478	adhP	-13.80	0.022588	200 -- 222	62 -- 83	ethanol-active dehydrogenase/acetaldehyde-active reductase	_____________199_____________________223\n_____________\|_______________________\|\n5'-GCA...GGAAC____AA____GC_______A___AGGAU...GUU-3'\n______________UAUG__GGCU__AGUUGUU_CGA\n______________:\|:\|__\|\|\|\|__\|\|\|\|:\|\|_\|\|\|\n______________GUGC__CCGA__UCAAUAA_GCU\n3'-CGC...UUCAA____AA____AA___________CAACU...AAG-5'\n_____________\|_______________________\|\n_____________84______________________61\n	212 -- 218	65 -- 71	-18.0685 kcal/mol	2.64248 kcal/mol	1.62352 kcal/mol	199 223@LB@ \| \|@LB@5'-GCA...GGAAC AA GC A AGGAU...GUU-3'@LB@ UAUG GGCU AGUUGUU CGA@LB@ :\|:\| \|\|\|\| \|\|\|\|:\|\| \|\|\|@LB@ GUGC CCGA UCAAUAA GCU@LB@3'-CGC...UUCAA AA AA CAACU...AAG-5'@LB@ \| \|@LB@ 84 61@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -18.0685 kcal/mol@LB@Unfolding Energy - mRNA 2.64248 kcal/mol@LB@Unfolding Energy - sRNA 1.62352 kcal/mol@LB@@LB@Position - mRNA 200 -- 222@LB@Position - sRNA 62 -- 83@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 65 -- 71@LB@
108	0.0187	0.5385	b1210	hemA	-9.14	0.148366	174 -- 184	75 -- 84	glutamyl tRNA reductase	_____________173_________185\n_____________\|___________\|\n5'-CCU...CCCUA__A________AUUAU...ACA-3'\n______________UC_ACGUUGGU\n______________\|\|_\|\|\|\|\|\|\|:\n______________AG_UGCAACCG\n3'-CGC...UUUCA___________AAAUC...AAG-5'\n_____________\|___________\|\n_____________85__________74\n	178 -- 184	75 -- 81	-12.935 kcal/mol	3.29275 kcal/mol	0.505918 kcal/mol	173 185@LB@ \| \|@LB@5'-CCU...CCCUA A AUUAU...ACA-3'@LB@ UC ACGUUGGU@LB@ \|\| \|\|\|\|\|\|\|:@LB@ AG UGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -12.935 kcal/mol@LB@Unfolding Energy - mRNA 3.29275 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 174 -- 184@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 75 -- 81@LB@
109	0.0187	0.5385	b2616	recN	-10.46	0.088138	200 -- 208	75 -- 83	recombination and repair protein	_____________199_______209\n_____________\|_________\|\n5'-UGA...ACGAC_________ACAAC...CGG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	202 -- 208	75 -- 81	-13.4657 kcal/mol	2.51607 kcal/mol	0.492259 kcal/mol	199 209@LB@ \| \|@LB@5'-UGA...ACGAC ACAAC...CGG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -13.4657 kcal/mol@LB@Unfolding Energy - mRNA 2.51607 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 200 -- 208@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 75 -- 81@LB@
110	0.0189	0.5385	b3175	secG	-9.72	0.118042	86 -- 106	67 -- 90	preprotein translocase membrane subunit	_____________85_______________________107\n_____________\|________________________\|\n5'-GCG...CUUGC__________UC____________GUAUU...CCU-3'\n______________GAAGG_UCAU____GCUUUGGUUA\n______________:\|\|:\|_\|\|\|:____\|\|\|\|\|:\|\|\|\|\n______________UUUUC_AGUG____CGAAAUCAAU\n3'-CGC...AGGCG_____A____CAAC__________AAGCU...AAG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	100 -- 106	67 -- 73	-15.607 kcal/mol	5.31183 kcal/mol	0.573552 kcal/mol	85 107@LB@ \| \|@LB@5'-GCG...CUUGC UC GUAUU...CCU-3'@LB@ GAAGG UCAU GCUUUGGUUA@LB@ :\|\|:\| \|\|\|: \|\|\|\|\|:\|\|\|\|@LB@ UUUUC AGUG CGAAAUCAAU@LB@3'-CGC...AGGCG A CAAC AAGCU...AAG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -9.72 kcal/mol@LB@Hybridization Energy -15.607 kcal/mol@LB@Unfolding Energy - mRNA 5.31183 kcal/mol@LB@Unfolding Energy - sRNA 0.573552 kcal/mol@LB@@LB@Position - mRNA 86 -- 106@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 67 -- 73@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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