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
191	0.03353	0.5559	b2129	yehX	-7.36	0.287226	59 -- 67	69 -- 77	putative ABC transporter ATPase	_____________58________68\n_____________\|_________\|\n5'-GGU...CAGGC_________GCGCU...UUG-3'\n______________GGUUUUGGU\n______________\|\|:\|\|\|:\|\|\n______________CCGAAAUCA\n3'-CGC...UGCAA_________AUAAG...AAG-5'\n_____________\|_________\|\n_____________78________68\n	61 -- 67	69 -- 75	-10.3561 kcal/mol	2.74802 kcal/mol	0.243235 kcal/mol	58 68@LB@ \| \|@LB@5'-GGU...CAGGC GCGCU...UUG-3'@LB@ GGUUUUGGU@LB@ \|\|:\|\|\|:\|\|@LB@ CCGAAAUCA@LB@3'-CGC...UGCAA AUAAG...AAG-5'@LB@ \| \|@LB@ 78 68@LB@@LB@@LB@Energy -7.36 kcal/mol@LB@Hybridization Energy -10.3561 kcal/mol@LB@Unfolding Energy - mRNA 2.74802 kcal/mol@LB@Unfolding Energy - sRNA 0.243235 kcal/mol@LB@@LB@Position - mRNA 59 -- 67@LB@Position - sRNA 69 -- 77@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 69 -- 75@LB@
148	0.0249	0.5467	b2131	osmF	-10.26	0.095288	236 -- 244	75 -- 83	putative ABC transporter periplasmic binding protein	_____________235_______245\n_____________\|_________\|\n5'-AGG...CUGGU_________AGCCG...UCG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	238 -- 244	75 -- 81	-12.6611 kcal/mol	1.90691 kcal/mol	0.492259 kcal/mol	235 245@LB@ \| \|@LB@5'-AGG...CUGGU AGCCG...UCG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -12.6611 kcal/mol@LB@Unfolding Energy - mRNA 1.90691 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 236 -- 244@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 75 -- 81@LB@
27	0.005053	0.5385	b2058	wcaB	-11.44	0.059229	168 -- 190	61 -- 82	putative acyl transferase	_____________167______________________191\n_____________\|________________________\|\n5'-ACC...GGCAA____C_____GA____________GGCGC...AGA-3'\n______________ACGU_UGGCU__UGG_UAUUCGGG\n______________\|\|\|\|_\|\|\|\|\|__\|:\|_\|\|\|\|\|\|:\|\n______________UGCA_ACCGA__AUC_AUAAGCUC\n3'-CGC...UCAAG__________A____A________AACUC...AAG-5'\n_____________\|________________________\|\n_____________83_______________________60\n	184 -- 190	61 -- 67	-21.3941 kcal/mol	8.91056 kcal/mol	1.03929 kcal/mol	167 191@LB@ \| \|@LB@5'-ACC...GGCAA C GA GGCGC...AGA-3'@LB@ ACGU UGGCU UGG UAUUCGGG@LB@ \|\|\|\| \|\|\|\|\| \|:\| \|\|\|\|\|\|:\|@LB@ UGCA ACCGA AUC AUAAGCUC@LB@3'-CGC...UCAAG A A AACUC...AAG-5'@LB@ \| \|@LB@ 83 60@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -21.3941 kcal/mol@LB@Unfolding Energy - mRNA 8.91056 kcal/mol@LB@Unfolding Energy - sRNA 1.03929 kcal/mol@LB@@LB@Position - mRNA 168 -- 190@LB@Position - sRNA 61 -- 82@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 61 -- 67@LB@
73	0.0135	0.5385	b3362	yhfG	-12.23	0.043008	184 -- 212	50 -- 86	putative antitoxin for Fic	_____________183___________________________________213\n_____________\|_____________________________________\|\n5'-GAU...GACAC_____G_GA___A__________A___GA________ACCGA...CUU-3'\n______________GUUCA_G__GGC_________UC_AGU__AGAAACUC\n______________\|\|\|\|\|_\|__\|\|\|_________\|\|_\|\|\|__\|\|\|\|\|\|\|\|\n______________CAAGU_C__CCG_________AG_UCA__UCUUUGAG\n3'-CGC...GUUUU_____G_AA___AAAUCAAUA__C___AC________AGCUU...AAG-5'\n_____________\|_____________________________________\|\n_____________87____________________________________49\n	206 -- 212	50 -- 56	-25.6976 kcal/mol	9.05881 kcal/mol	4.40785 kcal/mol	183 213@LB@ \| \|@LB@5'-GAU...GACAC G GA A A GA ACCGA...CUU-3'@LB@ GUUCA G GGC UC AGU AGAAACUC@LB@ \|\|\|\|\| \| \|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CAAGU C CCG AG UCA UCUUUGAG@LB@3'-CGC...GUUUU G AA AAAUCAAUA C AC AGCUU...AAG-5'@LB@ \| \|@LB@ 87 49@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -25.6976 kcal/mol@LB@Unfolding Energy - mRNA 9.05881 kcal/mol@LB@Unfolding Energy - sRNA 4.40785 kcal/mol@LB@@LB@Position - mRNA 184 -- 212@LB@Position - sRNA 50 -- 86@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 50 -- 56@LB@
166	0.02918	0.5559	b3518	yhjA	-9.21	0.144312	113 -- 127	71 -- 85	putative cytochrome C peroxidase	_____________112_____________128\n_____________\|_______________\|\n5'-CCG...UGUUU______A________UCUCG...GCA-3'\n______________UUUAUG_UGGCUUUG\n______________\|\|:\|:\|_\|\|\|\|\|\|\|:\n______________AAGUGC_ACCGAAAU\n3'-CGC...UUUUC______A________CAAUA...AAG-5'\n_____________\|_______________\|\n_____________86______________70\n	121 -- 127	71 -- 77	-14.7899 kcal/mol	5.0213 kcal/mol	0.560731 kcal/mol	112 128@LB@ \| \|@LB@5'-CCG...UGUUU A UCUCG...GCA-3'@LB@ UUUAUG UGGCUUUG@LB@ \|\|:\|:\| \|\|\|\|\|\|\|:@LB@ AAGUGC ACCGAAAU@LB@3'-CGC...UUUUC A CAAUA...AAG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -9.21 kcal/mol@LB@Hybridization Energy -14.7899 kcal/mol@LB@Unfolding Energy - mRNA 5.0213 kcal/mol@LB@Unfolding Energy - sRNA 0.560731 kcal/mol@LB@@LB@Position - mRNA 113 -- 127@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 71 -- 77@LB@
66	0.01284	0.5385	b1645	ydhK	-10.57	0.084210	155 -- 164	75 -- 84	putative efflux protein (PET) component of YdhJK efflux pump	_____________154________165\n_____________\|__________\|\n5'-CAG...CGAUG__________GUCGG...UGG-3'\n______________UCACGUUGGU\n______________\|\|\|\|\|\|\|\|\|:\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	158 -- 164	75 -- 81	-15.7281 kcal/mol	4.6508 kcal/mol	0.505918 kcal/mol	154 165@LB@ \| \|@LB@5'-CAG...CGAUG GUCGG...UGG-3'@LB@ UCACGUUGGU@LB@ \|\|\|\|\|\|\|\|\|:@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -15.7281 kcal/mol@LB@Unfolding Energy - mRNA 4.6508 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 155 -- 164@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 75 -- 81@LB@
100	0.01671	0.5385	b3211	yhcC	-9.80	0.114390	283 -- 295	70 -- 82	putative Fe-S oxidoreductase Radical SAM superfamily protein	_____________282___________296\n_____________\|_____________\|\n5'-UGC...GCUGC___GC________CUGCC-3'\n______________ACG__GGUUUUAG\n______________\|\|\|__\|\|:\|\|\|\|\|\n______________UGC__CCGAAAUC\n3'-CGC...UCAAG___AA________AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	289 -- 295	70 -- 76	-11.7424 kcal/mol	1.55142 kcal/mol	0.389672 kcal/mol	282 296@LB@ \| \|@LB@5'-UGC...GCUGC GC CUGCC-3'@LB@ ACG GGUUUUAG@LB@ \|\|\| \|\|:\|\|\|\|\|@LB@ UGC CCGAAAUC@LB@3'-CGC...UCAAG AA AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -9.80 kcal/mol@LB@Hybridization Energy -11.7424 kcal/mol@LB@Unfolding Energy - mRNA 1.55142 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 70 -- 76@LB@
192	0.03364	0.5559	b2333	yfcP	-8.48	0.190877	22 -- 36	61 -- 77	putative fimbrial-like adhesin protein	_____________21________________37\n_____________\|_________________\|\n5'-GCA...UACCC_________A_______CUUCA...AUU-3'\n______________GGUUUUGGU___UCGAG\n______________\|\|:\|\|\|:\|\|___\|\|\|\|\|\n______________CCGAAAUCA___AGCUC\n3'-CGC...UGCAA_________AUA_____AACUC...AAG-5'\n_____________\|_________________\|\n_____________78________________60\n	23 -- 29	70 -- 76	-16.4218 kcal/mol	7.14733 kcal/mol	0.796269 kcal/mol	21 37@LB@ \| \|@LB@5'-GCA...UACCC A CUUCA...AUU-3'@LB@ GGUUUUGGU UCGAG@LB@ \|\|:\|\|\|:\|\| \|\|\|\|\|@LB@ CCGAAAUCA AGCUC@LB@3'-CGC...UGCAA AUA AACUC...AAG-5'@LB@ \| \|@LB@ 78 60@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -16.4218 kcal/mol@LB@Unfolding Energy - mRNA 7.14733 kcal/mol@LB@Unfolding Energy - sRNA 0.796269 kcal/mol@LB@@LB@Position - mRNA 22 -- 36@LB@Position - sRNA 61 -- 77@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 70 -- 76@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@
55	0.01095	0.5385	b1220	ychO	-5.56	0.517016	132 -- 175	64 -- 91	putative invasin	_____________131__________________________________________176\n_____________\|____________________________________________\|\n5'-UCA...UACGA________GCCAGUAAU____AUUCUUUAA____A_____U___AUUAU...CAA-3'\n______________CAAAAGUU_________CGUU_________GGCU_UGGUU_UUC\n______________\|\|\|\|\|\|\|\|_________\|\|\|\|_________\|\|\|\|_\|:\|\|\|_\|\|\|\n______________GUUUUCAA_________GCAA_________CCGA_AUCAA_AAG\n3'-CGC...UAGGC________GU________________________A_____U___CUCAA...AAG-5'\n_____________\|____________________________________________\|\n_____________92___________________________________________63\n	133 -- 139	84 -- 90	-16.5622 kcal/mol	8.12255 kcal/mol	2.88465 kcal/mol	131 176@LB@ \| \|@LB@5'-UCA...UACGA GCCAGUAAU AUUCUUUAA A U AUUAU...CAA-3'@LB@ CAAAAGUU CGUU GGCU UGGUU UUC@LB@ \|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\| \|:\|\|\| \|\|\|@LB@ GUUUUCAA GCAA CCGA AUCAA AAG@LB@3'-CGC...UAGGC GU A U CUCAA...AAG-5'@LB@ \| \|@LB@ 92 63@LB@@LB@@LB@Energy -5.56 kcal/mol@LB@Hybridization Energy -16.5622 kcal/mol@LB@Unfolding Energy - mRNA 8.12255 kcal/mol@LB@Unfolding Energy - sRNA 2.88465 kcal/mol@LB@@LB@Position - mRNA 132 -- 175@LB@Position - sRNA 64 -- 91@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 84 -- 90@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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