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
128	0.02183	0.5385	b0874	ybjE	-9.13	0.148469	198 -- 230	59 -- 85	putative transporter	_____________197_______________________________231\n_____________\|_________________________________\|\n5'-GGG...GGGUU________UUCUG____GUUAAUC____U____CCCCU...UAA-3'\n______________UUCAUGUU_____GGCU_______AUUC_GGUU\n______________\|\|\|\|:\|\|\|_____\|\|\|\|_______\|\|\|\|_:\|\|\|\n______________AAGUGCAA_____CCGA_______UAAG_UCAA\n3'-CGC...UUUUC_________________AAUCAA_____C____CUCUU...AAG-5'\n_____________\|_________________________________\|\n_____________86________________________________58\n	199 -- 205	78 -- 84	-15.801 kcal/mol	4.95896 kcal/mol	1.70749 kcal/mol	197 231@LB@ \| \|@LB@5'-GGG...GGGUU UUCUG GUUAAUC U CCCCU...UAA-3'@LB@ UUCAUGUU GGCU AUUC GGUU@LB@ \|\|\|\|:\|\|\| \|\|\|\| \|\|\|\| :\|\|\|@LB@ AAGUGCAA CCGA UAAG UCAA@LB@3'-CGC...UUUUC AAUCAA C CUCUU...AAG-5'@LB@ \| \|@LB@ 86 58@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -15.801 kcal/mol@LB@Unfolding Energy - mRNA 4.95896 kcal/mol@LB@Unfolding Energy - sRNA 1.70749 kcal/mol@LB@@LB@Position - mRNA 198 -- 230@LB@Position - sRNA 59 -- 85@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 78 -- 84@LB@
91	0.0156	0.5385	b0881	clpS	-13.09	0.030255	248 -- 265	74 -- 90	regulatory protein for ClpA substrate specificity	_____________247________________266\n_____________\|__________________\|\n5'-GCA...GAAGA___________AC_C___AAAAC...UCA-3'\n______________AAAAGUUCGCG__G_GCU\n______________\|\|\|\|\|\|\|\|:\|\|__\|_\|\|\|\n______________UUUUCAAGUGC__C_CGA\n3'-CGC...AGGCG___________AA_____AAUCA...AAG-5'\n_____________\|__________________\|\n_____________91_________________73\n	252 -- 258	80 -- 86	-16.9257 kcal/mol	3.31752 kcal/mol	0.517587 kcal/mol	247 266@LB@ \| \|@LB@5'-GCA...GAAGA AC C AAAAC...UCA-3'@LB@ AAAAGUUCGCG G GCU@LB@ \|\|\|\|\|\|\|\|:\|\| \| \|\|\|@LB@ UUUUCAAGUGC C CGA@LB@3'-CGC...AGGCG AA AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -13.09 kcal/mol@LB@Hybridization Energy -16.9257 kcal/mol@LB@Unfolding Energy - mRNA 3.31752 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 248 -- 265@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 80 -- 86@LB@
152	0.02564	0.5485	b0887	cydD	-10.22	0.096853	263 -- 271	74 -- 82	glutathione/cysteine ABC transporter export permease/ATPase	_____________262_______272\n_____________\|_________\|\n5'-AUU...UCCCA_________GAAUA...UGA-3'\n______________ACGUUGGCU\n______________\|\|\|\|\|\|\|\|\|\n______________UGCAACCGA\n3'-CGC...UCAAG_________AAUCA...AAG-5'\n_____________\|_________\|\n_____________83________73\n	265 -- 271	74 -- 80	-15.056 kcal/mol	4.4924 kcal/mol	0.342466 kcal/mol	262 272@LB@ \| \|@LB@5'-AUU...UCCCA GAAUA...UGA-3'@LB@ ACGUUGGCU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UGCAACCGA@LB@3'-CGC...UCAAG AAUCA...AAG-5'@LB@ \| \|@LB@ 83 73@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -15.056 kcal/mol@LB@Unfolding Energy - mRNA 4.4924 kcal/mol@LB@Unfolding Energy - sRNA 0.342466 kcal/mol@LB@@LB@Position - mRNA 263 -- 271@LB@Position - sRNA 74 -- 82@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 74 -- 80@LB@
14	0.002739	0.5385	b0903	pflB	-11.82	0.050867	80 -- 105	57 -- 81	formate C-acetyltransferase 1 anaerobic; pyruvate formate-lyase 1	_____________79_________________________106\n_____________\|__________________________\|\n5'-CAC...AUUAU__G____GGUUU____G_________CAUAC...ACU-3'\n______________CG_UGGU_____GUUG_UUGGGUUGA\n______________\|\|_\|\|\|:_____\|\|\|:_\|:\|:\|\|\|\|\|\n______________GC_ACCG_____CAAU_AGCUCAACU\n3'-CGC...CAAGU__A____AAAU_____A_________CUUUG...AAG-5'\n_____________\|__________________________\|\n_____________82_________________________56\n	99 -- 105	57 -- 63	-19.5015 kcal/mol	6.38537 kcal/mol	1.29708 kcal/mol	79 106@LB@ \| \|@LB@5'-CAC...AUUAU G GGUUU G CAUAC...ACU-3'@LB@ CG UGGU GUUG UUGGGUUGA@LB@ \|\| \|\|\|: \|\|\|: \|:\|:\|\|\|\|\|@LB@ GC ACCG CAAU AGCUCAACU@LB@3'-CGC...CAAGU A AAAU A CUUUG...AAG-5'@LB@ \| \|@LB@ 82 56@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -19.5015 kcal/mol@LB@Unfolding Energy - mRNA 6.38537 kcal/mol@LB@Unfolding Energy - sRNA 1.29708 kcal/mol@LB@@LB@Position - mRNA 80 -- 105@LB@Position - sRNA 57 -- 81@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 57 -- 63@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@
74	0.01362	0.5385	b0946	zapC	-12.02	0.046851	175 -- 197	15 -- 35	FtsZ stabilizer	_____________174_____________________198\n_____________\|_______________________\|\n5'-AUU...GCUGC_______U_____AG________CAGAU...GUU-3'\n______________GGUUUUA_AGGGU__GGGAGAGG\n______________\|::\|\|:\|_\|\|\|\|\|__:::\|\|\|\|\|\n______________CUGAAGU_UCCCA__UUUUCUCC\n3'-CGC...CGUCA_____________A_________ACGGC...AAG-5'\n_____________\|_______________________\|\n_____________36______________________14\n	191 -- 197	15 -- 21	-19.3355 kcal/mol	3.98393 kcal/mol	3.33058 kcal/mol	174 198@LB@ \| \|@LB@5'-AUU...GCUGC U AG CAGAU...GUU-3'@LB@ GGUUUUA AGGGU GGGAGAGG@LB@ \|::\|\|:\| \|\|\|\|\| :::\|\|\|\|\|@LB@ CUGAAGU UCCCA UUUUCUCC@LB@3'-CGC...CGUCA A ACGGC...AAG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -19.3355 kcal/mol@LB@Unfolding Energy - mRNA 3.98393 kcal/mol@LB@Unfolding Energy - sRNA 3.33058 kcal/mol@LB@@LB@Position - mRNA 175 -- 197@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 15 -- 21@LB@
32	0.005403	0.5385	b0951	pqiB	-10.24	0.095947	95 -- 108	69 -- 82	paraquat-inducible SoxRS-regulated MCE domain protein	_____________94_____________109\n_____________\|______________\|\n5'-CUG...CAUUA_____U________CGUCA...UUC-3'\n______________AUGUU_GCUUUAGU\n______________\|:\|\|\|_\|\|\|\|\|\|\|\|\n______________UGCAA_CGAAAUCA\n3'-CGC...UCAAG_____C________AUAAG...AAG-5'\n_____________\|______________\|\n_____________83_____________68\n	102 -- 108	69 -- 75	-13.4891 kcal/mol	2.8545 kcal/mol	0.389912 kcal/mol	94 109@LB@ \| \|@LB@5'-CUG...CAUUA U CGUCA...UUC-3'@LB@ AUGUU GCUUUAGU@LB@ \|:\|\|\| \|\|\|\|\|\|\|\|@LB@ UGCAA CGAAAUCA@LB@3'-CGC...UCAAG C AUAAG...AAG-5'@LB@ \| \|@LB@ 83 68@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -13.4891 kcal/mol@LB@Unfolding Energy - mRNA 2.8545 kcal/mol@LB@Unfolding Energy - sRNA 0.389912 kcal/mol@LB@@LB@Position - mRNA 95 -- 108@LB@Position - sRNA 69 -- 82@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 69 -- 75@LB@
196	0.0344	0.5559	b0954	fabA	-7.50	0.274211	100 -- 110	74 -- 84	beta-hydroxydecanoyl thioester dehydrase	_____________99__________111\n_____________\|___________\|\n5'-GUG...GGCCA___________GAACU...ACA-3'\n______________UUACGUUGGCU\n______________\|:\|\|\|\|\|\|\|\|\|\n______________AGUGCAACCGA\n3'-CGC...UUUCA___________AAUCA...AAG-5'\n_____________\|___________\|\n_____________85__________73\n	104 -- 110	74 -- 80	-16.8122 kcal/mol	8.80896 kcal/mol	0.508159 kcal/mol	99 111@LB@ \| \|@LB@5'-GUG...GGCCA GAACU...ACA-3'@LB@ UUACGUUGGCU@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ AGUGCAACCGA@LB@3'-CGC...UUUCA AAUCA...AAG-5'@LB@ \| \|@LB@ 85 73@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -16.8122 kcal/mol@LB@Unfolding Energy - mRNA 8.80896 kcal/mol@LB@Unfolding Energy - sRNA 0.508159 kcal/mol@LB@@LB@Position - mRNA 100 -- 110@LB@Position - sRNA 74 -- 84@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 74 -- 80@LB@
156	0.02672	0.5559	b0957	ompA	-9.60	0.124024	22 -- 30	81 -- 89	outer membrane protein A (3a;II*;G;d)	_____________21________31\n_____________\|_________\|\n5'-CUU...CUGAC_________ACUUG...AAC-3'\n______________GGAGUUCAC\n______________::\|\|\|\|\|\|\|\n______________UUUCAAGUG\n3'-CGC...GGCGU_________CAACC...AAG-5'\n_____________\|_________\|\n_____________90________80\n	24 -- 30	81 -- 87	-11.1644 kcal/mol	1.067 kcal/mol	0.501582 kcal/mol	21 31@LB@ \| \|@LB@5'-CUU...CUGAC ACUUG...AAC-3'@LB@ GGAGUUCAC@LB@ ::\|\|\|\|\|\|\|@LB@ UUUCAAGUG@LB@3'-CGC...GGCGU CAACC...AAG-5'@LB@ \| \|@LB@ 90 80@LB@@LB@@LB@Energy -9.60 kcal/mol@LB@Hybridization Energy -11.1644 kcal/mol@LB@Unfolding Energy - mRNA 1.067 kcal/mol@LB@Unfolding Energy - sRNA 0.501582 kcal/mol@LB@@LB@Position - mRNA 22 -- 30@LB@Position - sRNA 81 -- 89@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 81 -- 87@LB@
120	0.02045	0.5385	b0979	cbdB	-12.05	0.046235	177 -- 194	16 -- 34	cytochrome bd-II oxidase subunit II	_____________176_________________195\n_____________\|___________________\|\n5'-AUA...ACGCA__AA_______________AAAAU...GCU-3'\n______________GC__CAGGGG_UAAAGGAG\n______________:\|__\|\|:\|\|\|_\|\|\|\|:\|\|\|\n______________UG__GUUCCC_AUUUUCUC\n3'-CGC...GUCAC__AA______A________CACGG...AAG-5'\n_____________\|___________________\|\n_____________35__________________15\n	188 -- 194	16 -- 22	-18.7902 kcal/mol	3.40633 kcal/mol	3.33043 kcal/mol	176 195@LB@ \| \|@LB@5'-AUA...ACGCA AA AAAAU...GCU-3'@LB@ GC CAGGGG UAAAGGAG@LB@ :\| \|\|:\|\|\| \|\|\|\|:\|\|\|@LB@ UG GUUCCC AUUUUCUC@LB@3'-CGC...GUCAC AA A CACGG...AAG-5'@LB@ \| \|@LB@ 35 15@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -18.7902 kcal/mol@LB@Unfolding Energy - mRNA 3.40633 kcal/mol@LB@Unfolding Energy - sRNA 3.33043 kcal/mol@LB@@LB@Position - mRNA 177 -- 194@LB@Position - sRNA 16 -- 34@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 16 -- 22@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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