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
170	0.03041	0.5559	b1629	rsxC	-10.04	0.103937	197 -- 215	64 -- 83	SoxR iron-sulfur cluster reduction factor component; putative membrane-associated NADH oxidoreductase of electron transport complex	_____________196__________________216\n_____________\|____________________\|\n5'-UCA...UGGAA___CAU_____A________UCUGC...CCC-3'\n______________CAC____GCUU_AGUUAUUC\n______________\|\|\|____\|\|\|\|_\|\|\|\|\|\|\|\|\n______________GUG____CGAA_UCAAUAAG\n3'-CGC...UUCAA___CAAC____A________CUCAA...AAG-5'\n_____________\|____________________\|\n_____________84___________________63\n	209 -- 215	64 -- 70	-13.7112 kcal/mol	3.10702 kcal/mol	0.560651 kcal/mol	196 216@LB@ \| \|@LB@5'-UCA...UGGAA CAU A UCUGC...CCC-3'@LB@ CAC GCUU AGUUAUUC@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUG CGAA UCAAUAAG@LB@3'-CGC...UUCAA CAAC A CUCAA...AAG-5'@LB@ \| \|@LB@ 84 63@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -13.7112 kcal/mol@LB@Unfolding Energy - mRNA 3.10702 kcal/mol@LB@Unfolding Energy - sRNA 0.560651 kcal/mol@LB@@LB@Position - mRNA 197 -- 215@LB@Position - sRNA 64 -- 83@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 64 -- 70@LB@
80	0.01445	0.5385	b4257	yjgN	-10.51	0.086376	202 -- 215	65 -- 78	DUF898 family inner membrane protein	_____________201____________216\n_____________\|______________\|\n5'-UUA...UUUUA_____CA_______AAUGA...UGU-3'\n______________UGGCU__AGUUAUU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\n______________ACCGA__UCAAUAA\n3'-CGC...GUGCA_____AA_______GCUCA...AAG-5'\n_____________\|______________\|\n_____________79_____________64\n	209 -- 215	65 -- 71	-13.5706 kcal/mol	2.80573 kcal/mol	0.256929 kcal/mol	201 216@LB@ \| \|@LB@5'-UUA...UUUUA CA AAUGA...UGU-3'@LB@ UGGCU AGUUAUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ ACCGA UCAAUAA@LB@3'-CGC...GUGCA AA GCUCA...AAG-5'@LB@ \| \|@LB@ 79 64@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -13.5706 kcal/mol@LB@Unfolding Energy - mRNA 2.80573 kcal/mol@LB@Unfolding Energy - sRNA 0.256929 kcal/mol@LB@@LB@Position - mRNA 202 -- 215@LB@Position - sRNA 65 -- 78@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 65 -- 71@LB@
72	0.0135	0.5385	b1117	lolD	-8.66	0.177865	184 -- 202	66 -- 83	outer membrane-specific lipoprotein transporter subunit	_____________183_________________203\n_____________\|___________________\|\n5'-GCU...CAACC___UGA_______C_____GAAUA...GCG-3'\n______________CGC___GGCUUUA_GUUAU\n______________\|:\|___\|\|\|\|\|\|\|_\|\|\|\|\|\n______________GUG___CCGAAAU_CAAUA\n3'-CGC...UUCAA___CAA_____________AGCUC...AAG-5'\n_____________\|___________________\|\n_____________84__________________65\n	190 -- 196	71 -- 77	-15.2298 kcal/mol	6.00943 kcal/mol	0.556032 kcal/mol	183 203@LB@ \| \|@LB@5'-GCU...CAACC UGA C GAAUA...GCG-3'@LB@ CGC GGCUUUA GUUAU@LB@ \|:\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ GUG CCGAAAU CAAUA@LB@3'-CGC...UUCAA CAA AGCUC...AAG-5'@LB@ \| \|@LB@ 84 65@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -15.2298 kcal/mol@LB@Unfolding Energy - mRNA 6.00943 kcal/mol@LB@Unfolding Energy - sRNA 0.556032 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 66 -- 83@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 71 -- 77@LB@
98	0.0165	0.5385	b0151	fhuC	-12.15	0.044517	184 -- 202	66 -- 85	iron(3+)-hydroxamate import ABC transporter ATPase	_____________183____________________203\n_____________\|______________________\|\n5'-CUG...CCCAU_____AA_______________GCAGG...CCU-3'\n______________UUCAC__GUUGGCU___GUUAU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|___\|\|\|\|\|\n______________AAGUG__CAACCGA___CAAUA\n3'-CGC...UUUUC______________AAU_____AGCUC...AAG-5'\n_____________\|______________________\|\n_____________86_____________________65\n	191 -- 197	74 -- 80	-16.912 kcal/mol	4.1925 kcal/mol	0.573112 kcal/mol	183 203@LB@ \| \|@LB@5'-CUG...CCCAU AA GCAGG...CCU-3'@LB@ UUCAC GUUGGCU GUUAU@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AAGUG CAACCGA CAAUA@LB@3'-CGC...UUUUC AAU AGCUC...AAG-5'@LB@ \| \|@LB@ 86 65@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -16.912 kcal/mol@LB@Unfolding Energy - mRNA 4.1925 kcal/mol@LB@Unfolding Energy - sRNA 0.573112 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 66 -- 85@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 74 -- 80@LB@
195	0.03428	0.5559	b0434	yajG	-10.30	0.093744	131 -- 149	66 -- 84	putative lipoprotein	_____________130__________________150\n_____________\|____________________\|\n5'-UGG...UCCCC___C_______AAU______GAUGG...UGC-3'\n______________UCG_CGUUGGC____GUUAU\n______________\|\|:_\|\|\|\|\|\|\|____\|\|\|\|\|\n______________AGU_GCAACCG____CAAUA\n3'-CGC...UUUCA___________AAAU_____AGCUC...AAG-5'\n_____________\|____________________\|\n_____________85___________________65\n	135 -- 141	75 -- 81	-17.0927 kcal/mol	6.21917 kcal/mol	0.5705 kcal/mol	130 150@LB@ \| \|@LB@5'-UGG...UCCCC C AAU GAUGG...UGC-3'@LB@ UCG CGUUGGC GUUAU@LB@ \|\|: \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AGU GCAACCG CAAUA@LB@3'-CGC...UUUCA AAAU AGCUC...AAG-5'@LB@ \| \|@LB@ 85 65@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -17.0927 kcal/mol@LB@Unfolding Energy - mRNA 6.21917 kcal/mol@LB@Unfolding Energy - sRNA 0.5705 kcal/mol@LB@@LB@Position - mRNA 131 -- 149@LB@Position - sRNA 66 -- 84@LB@Position Seed - mRNA 135 -- 141@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@
176	0.03112	0.5559	b2536	hcaT	-7.63	0.261550	240 -- 259	67 -- 85	putative 3-phenylpropionic transporter	_____________239__________________260\n_____________\|____________________\|\n5'-UCG...GCUAU_____AUACUU_________CGGCA...GGA-3'\n______________UUCAC______UUUUAGUUA\n______________\|\|\|\|\|______:\|\|\|\|\|\|\|\|\n______________AAGUG______GAAAUCAAU\n3'-CGC...UUUUC_____CAACC__________AAGCU...AAG-5'\n_____________\|____________________\|\n_____________86___________________66\n	253 -- 259	67 -- 73	-10.0019 kcal/mol	1.80629 kcal/mol	0.569003 kcal/mol	239 260@LB@ \| \|@LB@5'-UCG...GCUAU AUACUU CGGCA...GGA-3'@LB@ UUCAC UUUUAGUUA@LB@ \|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ AAGUG GAAAUCAAU@LB@3'-CGC...UUUUC CAACC AAGCU...AAG-5'@LB@ \| \|@LB@ 86 66@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -10.0019 kcal/mol@LB@Unfolding Energy - mRNA 1.80629 kcal/mol@LB@Unfolding Energy - sRNA 0.569003 kcal/mol@LB@@LB@Position - mRNA 240 -- 259@LB@Position - sRNA 67 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 67 -- 73@LB@
25	0.004715	0.5385	b0009	mog	-11.66	0.054310	209 -- 227	68 -- 85	molybdochelatase incorporating molybdenum into molybdopterin	_____________208__________________228\n_____________\|____________________\|\n5'-UGG...AAUAC_______AU___________UCCAU...CAU-3'\n______________UUUACGU__UGGC_UUAGUU\n______________\|\|:\|\|\|\|__\|\|\|\|_\|\|\|\|\|\|\n______________AAGUGCA__ACCG_AAUCAA\n3'-CGC...UUUUC_____________A______UAAGC...AAG-5'\n_____________\|____________________\|\n_____________86___________________67\n	209 -- 215	79 -- 85	-16.6663 kcal/mol	4.44065 kcal/mol	0.567776 kcal/mol	208 228@LB@ \| \|@LB@5'-UGG...AAUAC AU UCCAU...CAU-3'@LB@ UUUACGU UGGC UUAGUU@LB@ \|\|:\|\|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ AAGUGCA ACCG AAUCAA@LB@3'-CGC...UUUUC A UAAGC...AAG-5'@LB@ \| \|@LB@ 86 67@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -16.6663 kcal/mol@LB@Unfolding Energy - mRNA 4.44065 kcal/mol@LB@Unfolding Energy - sRNA 0.567776 kcal/mol@LB@@LB@Position - mRNA 209 -- 227@LB@Position - sRNA 68 -- 85@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 79 -- 85@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@
38	0.006978	0.5385	b3738	atpB	-10.53	0.085759	128 -- 143	69 -- 84	F0 sector of membrane-bound ATP synthase subunit a	_____________127______________144\n_____________\|________________\|\n5'-CAU...GAUCG______G_________GCUGG...ACC-3'\n______________UUACGU_GGUUUUGGU\n______________\|:\|\|\|\|_\|\|:\|\|\|:\|\|\n______________AGUGCA_CCGAAAUCA\n3'-CGC...UUUCA______A_________AUAAG...AAG-5'\n_____________\|________________\|\n_____________85_______________68\n	137 -- 143	69 -- 75	-16.8893 kcal/mol	5.79988 kcal/mol	0.563592 kcal/mol	127 144@LB@ \| \|@LB@5'-CAU...GAUCG G GCUGG...ACC-3'@LB@ UUACGU GGUUUUGGU@LB@ \|:\|\|\|\| \|\|:\|\|\|:\|\|@LB@ AGUGCA CCGAAAUCA@LB@3'-CGC...UUUCA A AUAAG...AAG-5'@LB@ \| \|@LB@ 85 68@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -16.8893 kcal/mol@LB@Unfolding Energy - mRNA 5.79988 kcal/mol@LB@Unfolding Energy - sRNA 0.563592 kcal/mol@LB@@LB@Position - mRNA 128 -- 143@LB@Position - sRNA 69 -- 84@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 69 -- 75@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)

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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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