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
102	0.003218	0.1101	b3816	corA	-9.85	0.049984	130 -- 160	4 -- 37	magnesium/nickel/cobalt transporter		_____________129_________________________________161\n_____________\|___________________________________\|\n5'-ACC...UUAAU_________CCCA________GUU___G_______ACCGA...AAC-3'\n______________GGUCUGAAA________AUUU___UCU_UGUGCCC\n______________\|\|\|\|\|\|\|\|\|________\|\|:\|___:\|\|_\|\|\|:\|\|\|\n______________CCAGACUUU________UAGA___GGA_ACAUGGG\n3'-AUU...AUUUU_________CUAUCUUG____AU____G_______AUG-5'\n_____________\|___________________________________\|\n_____________38__________________________________3\n	154 -- 160	4 -- 10	-28.4013 kcal/mol	7.22925 kcal/mol	11.3428 kcal/mol	129 161@LB@ \| \|@LB@5'-ACC...UUAAU CCCA GUU G ACCGA...AAC-3'@LB@ GGUCUGAAA AUUU UCU UGUGCCC@LB@ \|\|\|\|\|\|\|\|\| \|\|:\| :\|\| \|\|\|:\|\|\|@LB@ CCAGACUUU UAGA GGA ACAUGGG@LB@3'-AUU...AUUUU CUAUCUUG AU G AUG-5'@LB@ \| \|@LB@ 38 3@LB@@LB@@LB@Energy -9.85 kcal/mol@LB@Hybridization Energy -28.4013 kcal/mol@LB@Unfolding Energy - mRNA 7.22925 kcal/mol@LB@Unfolding Energy - sRNA 11.3428 kcal/mol@LB@@LB@Position - mRNA 130 -- 160@LB@Position - sRNA 4 -- 37@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 4 -- 10@LB@
66	0.001146	0.05856	b1657	ydhP	-3.95	0.782289	131 -- 139	49 -- 57	putative MFS transporter inner membrane protein		_____________130_______140\n_____________\|_________\|\n5'-UCG...UUUUU_G_______UGUCA...GCG-3'\n______________U_UGAUUGC\n______________\|_:\|\|\|\|:\|\n______________A_GCUAAUG\n3'-AUU...GGUUU_G_______CACUU...AUG-5'\n_____________\|_________\|\n_____________58________48\n	133 -- 139	49 -- 55	-6.30818 kcal/mol	2.04371 kcal/mol	0.318327 kcal/mol	130 140@LB@ \| \|@LB@5'-UCG...UUUUU G UGUCA...GCG-3'@LB@ U UGAUUGC@LB@ \| :\|\|\|\|:\|@LB@ A GCUAAUG@LB@3'-AUU...GGUUU G CACUU...AUG-5'@LB@ \| \|@LB@ 58 48@LB@@LB@@LB@Energy -3.95 kcal/mol@LB@Hybridization Energy -6.30818 kcal/mol@LB@Unfolding Energy - mRNA 2.04371 kcal/mol@LB@Unfolding Energy - sRNA 0.318327 kcal/mol@LB@@LB@Position - mRNA 131 -- 139@LB@Position - sRNA 49 -- 57@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 49 -- 55@LB@
8	1.842e-05	0.007771	b2797	sdaB	-15.07	0.000654	133 -- 147	55 -- 69	L-serine dehydratase 2		_____________132_____________148\n_____________\|_______________\|\n5'-CGA...CUCUC_______________UUUCG...UGA-3'\n______________UGUUCAGCUAAGUCC\n______________\|:\|\|\|\|\|\|:\|\|:\|\|\|\n______________AUAAGUCGGUUUAGG\n3'-AUU...AUUUU_______________CUAAU...AUG-5'\n_____________\|_______________\|\n_____________70______________54\n	141 -- 147	55 -- 61	-22.3059 kcal/mol	1.18067 kcal/mol	6.0797 kcal/mol	132 148@LB@ \| \|@LB@5'-CGA...CUCUC UUUCG...UGA-3'@LB@ UGUUCAGCUAAGUCC@LB@ \|:\|\|\|\|\|\|:\|\|:\|\|\|@LB@ AUAAGUCGGUUUAGG@LB@3'-AUU...AUUUU CUAAU...AUG-5'@LB@ \| \|@LB@ 70 54@LB@@LB@@LB@Energy -15.07 kcal/mol@LB@Hybridization Energy -22.3059 kcal/mol@LB@Unfolding Energy - mRNA 1.18067 kcal/mol@LB@Unfolding Energy - sRNA 6.0797 kcal/mol@LB@@LB@Position - mRNA 133 -- 147@LB@Position - sRNA 55 -- 69@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 55 -- 61@LB@
143	0.005218	0.1284	b1922	fliA	-8.86	0.094137	133 -- 141	50 -- 58	RNA polymerase sigma 28 (sigma F) factor		_____________132_______142\n_____________\|_________\|\n5'-AGG...UAAUC_________AAAAC...UUC-3'\n______________GUCCGAUUA\n______________:\|\|\|\|\|\|\|\|\n______________UAGGCUAAU\n3'-AUU...CGGUU_________GCACU...AUG-5'\n_____________\|_________\|\n_____________59________49\n	135 -- 141	50 -- 56	-11.3914 kcal/mol	2.23267 kcal/mol	0.317553 kcal/mol	132 142@LB@ \| \|@LB@5'-AGG...UAAUC AAAAC...UUC-3'@LB@ GUCCGAUUA@LB@ :\|\|\|\|\|\|\|\|@LB@ UAGGCUAAU@LB@3'-AUU...CGGUU GCACU...AUG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -11.3914 kcal/mol@LB@Unfolding Energy - mRNA 2.23267 kcal/mol@LB@Unfolding Energy - sRNA 0.317553 kcal/mol@LB@@LB@Position - mRNA 133 -- 141@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 50 -- 56@LB@
77	0.00159	0.07263	b2159	nfo	-11.23	0.018951	134 -- 154	4 -- 22	endonuclease IV with intrinsic 3'-5' exonuclease activity		_____________133___________________155\n_____________\|_____________________\|\n5'-GAC...CCACU__________C____UA____GCUAU...CCA-3'\n______________ACAUCUUGCU_CUGU__ACCC\n______________\|\|\|\|\|\|\|:\|:_\|\|\|\|__\|\|\|\|\n______________UGUAGAAUGG_GACA__UGGG\n3'-AUU...UAUCU__________A__________AUG-5'\n_____________\|_____________________\|\n_____________23____________________3\n	134 -- 140	16 -- 22	-23.2044 kcal/mol	4.007 kcal/mol	7.98841 kcal/mol	133 155@LB@ \| \|@LB@5'-GAC...CCACU C UA GCUAU...CCA-3'@LB@ ACAUCUUGCU CUGU ACCC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\| \|\|\|\|@LB@ UGUAGAAUGG GACA UGGG@LB@3'-AUU...UAUCU A AUG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -23.2044 kcal/mol@LB@Unfolding Energy - mRNA 4.007 kcal/mol@LB@Unfolding Energy - sRNA 7.98841 kcal/mol@LB@@LB@Position - mRNA 134 -- 154@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 16 -- 22@LB@
149	0.005967	0.1406	b0472	recR	-13.66	0.002580	134 -- 160	3 -- 29	gap repair protein		_____________133_________________________161\n_____________\|___________________________\|\n5'-GUG...AACGC___A____AAAAUG_____________CCGGA...UUC-3'\n______________AGA_AGAA______GCCUCUGUAUCCU\n______________\|\|\|_\|\|\|\|______:\|\|\|\|\|\|\|\|:\|\|\|\n______________UCU_UCUU______UGGAGACAUGGGA\n3'-AUU...GACUU___A____GUAGAA_____________UG-5'\n_____________\|___________________________\|\n_____________30__________________________2\n	154 -- 160	3 -- 9	-27.6106 kcal/mol	5.92472 kcal/mol	8.05021 kcal/mol	133 161@LB@ \| \|@LB@5'-GUG...AACGC A AAAAUG CCGGA...UUC-3'@LB@ AGA AGAA GCCUCUGUAUCCU@LB@ \|\|\| \|\|\|\| :\|\|\|\|\|\|\|\|:\|\|\|@LB@ UCU UCUU UGGAGACAUGGGA@LB@3'-AUU...GACUU A GUAGAA UG-5'@LB@ \| \|@LB@ 30 2@LB@@LB@@LB@Energy -13.66 kcal/mol@LB@Hybridization Energy -27.6106 kcal/mol@LB@Unfolding Energy - mRNA 5.92472 kcal/mol@LB@Unfolding Energy - sRNA 8.05021 kcal/mol@LB@@LB@Position - mRNA 134 -- 160@LB@Position - sRNA 3 -- 29@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 3 -- 9@LB@
84	0.002084	0.08729	b2067	yegE	-5.99	0.414041	137 -- 150	1 -- 15	putative diguanylate cyclase		_____________136_____________151\n_____________\|_______________\|\n5'-AGU...GUAAA___________A___AUAAA...CGC-3'\n______________ACUUUUGUACU__GC\n______________\|\|:\|:\|\|\|\|\|:__:\|\n______________UGGAGACAUGG__UG\n3'-AUU...UAGAA___________GA__-5'\n_____________\|______________\|\n_____________16_____________1\n	141 -- 147	5 -- 11	-13.6769 kcal/mol	1.88278 kcal/mol	5.82808 kcal/mol	136 151@LB@ \| \|@LB@5'-AGU...GUAAA A AUAAA...CGC-3'@LB@ ACUUUUGUACU GC@LB@ \|\|:\|:\|\|\|\|\|: :\|@LB@ UGGAGACAUGG UG@LB@3'-AUU...UAGAA GA -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -13.6769 kcal/mol@LB@Unfolding Energy - mRNA 1.88278 kcal/mol@LB@Unfolding Energy - sRNA 5.82808 kcal/mol@LB@@LB@Position - mRNA 137 -- 150@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 5 -- 11@LB@
100	0.003115	0.1096	b0353	mhpT	-8.28	0.132596	137 -- 146	48 -- 57	3-hydroxyphenylpropionic transporter		_____________136________147\n_____________\|__________\|\n5'-CGG...AUAGU__________CGGCU...CGG-3'\n______________UCUGAUUACG\n______________\|\|:\|\|\|\|\|\|\|\n______________AGGCUAAUGC\n3'-AUU...GGUUU__________ACUUC...AUG-5'\n_____________\|__________\|\n_____________58_________47\n	140 -- 146	48 -- 54	-13.4725 kcal/mol	3.61374 kcal/mol	1.55976 kcal/mol	136 147@LB@ \| \|@LB@5'-CGG...AUAGU CGGCU...CGG-3'@LB@ UCUGAUUACG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ AGGCUAAUGC@LB@3'-AUU...GGUUU ACUUC...AUG-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -8.28 kcal/mol@LB@Hybridization Energy -13.4725 kcal/mol@LB@Unfolding Energy - mRNA 3.61374 kcal/mol@LB@Unfolding Energy - sRNA 1.55976 kcal/mol@LB@@LB@Position - mRNA 137 -- 146@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 48 -- 54@LB@
51	0.0006491	0.04477	b3224	nanT	-16.25	0.000177	140 -- 151	1 -- 12	sialic acid transporter	b4279	_____________139__________152\n_____________\|____________\|\n5'-CGC...ACGCA____________AAUUU...GUU-3'\n______________UCUGUACCCUAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________AGACAUGGGAUG\n3'-AUU...AAUGG____________-5'\n_____________\|___________\|\n_____________13__________1\n	145 -- 151	1 -- 7	-21.6524 kcal/mol	1.93745 kcal/mol	3.49051 kcal/mol	139 152@LB@ \| \|@LB@5'-CGC...ACGCA AAUUU...GUU-3'@LB@ UCUGUACCCUAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ AGACAUGGGAUG@LB@3'-AUU...AAUGG -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -21.6524 kcal/mol@LB@Unfolding Energy - mRNA 1.93745 kcal/mol@LB@Unfolding Energy - sRNA 3.49051 kcal/mol@LB@@LB@Position - mRNA 140 -- 151@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 1 -- 7@LB@
181	0.007802	0.1516	b1797	yeaR	-7.07	0.254063	142 -- 149	2 -- 9	DUF1971 family protein nitrate-inducible		_____________141______150\n_____________\|________\|\n5'-UGC...CAGGC________AAACG...AAG-3'\n______________GUACCCUG\n______________\|\|\|\|\|\|\|:\n______________CAUGGGAU\n3'-AUU...GGAGA________G-5'\n_____________\|________\|\n_____________10_______1\n	143 -- 149	2 -- 8	-12.2602 kcal/mol	3.09143 kcal/mol	2.12684 kcal/mol	141 150@LB@ \| \|@LB@5'-UGC...CAGGC AAACG...AAG-3'@LB@ GUACCCUG@LB@ \|\|\|\|\|\|\|:@LB@ CAUGGGAU@LB@3'-AUU...GGAGA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.07 kcal/mol@LB@Hybridization Energy -12.2602 kcal/mol@LB@Unfolding Energy - mRNA 3.09143 kcal/mol@LB@Unfolding Energy - sRNA 2.12684 kcal/mol@LB@@LB@Position - mRNA 142 -- 149@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 143 -- 149@LB@Position Seed - sRNA 2 -- 8@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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