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
88	0.002339	0.09349	b3878	yihQ	-11.00	0.022508	260 -- 267	1 -- 8	putative sulpholipid alpha-glucosidase; alpha-glucosyl fluoride glucosidase	b3656	_____________259______268\n_____________\|________\|\n5'-AAC...AGUUU________AUUUU...GCA-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	261 -- 267	1 -- 7	-13.427 kcal/mol	0.33456 kcal/mol	2.11603 kcal/mol	259 268@LB@ \| \|@LB@5'-AAC...AGUUU AUUUU...GCA-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -13.427 kcal/mol@LB@Unfolding Energy - mRNA 0.33456 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 260 -- 267@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 1 -- 7@LB@
50	0.0006038	0.04249	b3755	yieP	-5.20	0.556147	189 -- 196	25 -- 32	putative transcriptional regulator		_____________188______197\n_____________\|________\|\n5'-UUC...AAAAA________AGUAA...CCG-3'\n______________GGAAGAUA\n______________\|:\|\|\|\|\|\|\n______________CUUUCUAU\n3'-AUU...CCAGA________CUUGU...AUG-5'\n_____________\|________\|\n_____________33_______24\n	190 -- 196	25 -- 31	-8.32385 kcal/mol	1.19727 kcal/mol	1.85262 kcal/mol	188 197@LB@ \| \|@LB@5'-UUC...AAAAA AGUAA...CCG-3'@LB@ GGAAGAUA@LB@ \|:\|\|\|\|\|\|@LB@ CUUUCUAU@LB@3'-AUU...CCAGA CUUGU...AUG-5'@LB@ \| \|@LB@ 33 24@LB@@LB@@LB@Energy -5.20 kcal/mol@LB@Hybridization Energy -8.32385 kcal/mol@LB@Unfolding Energy - mRNA 1.19727 kcal/mol@LB@Unfolding Energy - sRNA 1.85262 kcal/mol@LB@@LB@Position - mRNA 189 -- 196@LB@Position - sRNA 25 -- 32@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 25 -- 31@LB@
41	0.000458	0.03766	b3679	yidK	-16.91	0.000078	119 -- 159	1 -- 60	putative transporter		_____________118__________________________________________________________160\n_____________\|____________________________________________________________\|\n5'-UUU...UUUAA________C_____________________CCCGAC________________________AUUCA...AAG-3'\n______________GAAUCUGA_UGC______________CUGA________GCAUUUUACCUCU___CCCUAU\n______________:\|\|\|\|:\|\|_\|:\|______________\|\|\|\|________:\|\|\|:\|\|\|\|\|\|\|\|___\|\|\|\|\|:\n______________UUUAGGCU_AUG______________GACU________UGUAGAAUGGAGA___GGGAUG\n3'-AUU...GUCGG________A___CACUUCAUUUUCCA____UUCUAUCU_____________CAU______-5'\n_____________\|___________________________________________________________\|\n_____________61__________________________________________________________1\n	147 -- 153	10 -- 16	-34.139 kcal/mol	4.55251 kcal/mol	12.7042 kcal/mol	118 160@LB@ \| \|@LB@5'-UUU...UUUAA C CCCGAC AUUCA...AAG-3'@LB@ GAAUCUGA UGC CUGA GCAUUUUACCUCU CCCUAU@LB@ :\|\|\|\|:\|\| \|:\| \|\|\|\| :\|\|\|:\|\|\|\|\|\|\|\| \|\|\|\|\|:@LB@ UUUAGGCU AUG GACU UGUAGAAUGGAGA GGGAUG@LB@3'-AUU...GUCGG A CACUUCAUUUUCCA UUCUAUCU CAU -5'@LB@ \| \|@LB@ 61 1@LB@@LB@@LB@Energy -16.91 kcal/mol@LB@Hybridization Energy -34.139 kcal/mol@LB@Unfolding Energy - mRNA 4.55251 kcal/mol@LB@Unfolding Energy - sRNA 12.7042 kcal/mol@LB@@LB@Position - mRNA 119 -- 159@LB@Position - sRNA 1 -- 60@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 10 -- 16@LB@
60	0.0009057	0.0531	b2740	ygbN	-7.72	0.181404	16 -- 72	3 -- 58	putative transporter		_____________15__________________________________________________________73\n_____________\|___________________________________________________________\|\n5'-GUG...CGCCU_______G_G_____A__UC___G_____UC___UGU______AA__________G___CACCG...UCC-3'\n______________GUUCGAU_A_GUGGG_UA__AGG_CUGGA__GGU___GAAUAU___ACCUC_GUG_CCU\n______________:\|:\|\|\|\|_\|_\|\|\|::_\|\|__\|\|\|_\|\|\|:\|__\|:\|___\|\|\|:\|\|___\|\|\|\|\|_\|\|:_\|\|\|\n______________UAGGCUA_U_CACUU_AU__UCC_GACUU__CUA___CUUGUA___UGGAG_CAU_GGA\n3'-AUU...CGGUU_______A_G_____C__UU___A_____U____U________GAA_____A___G___UG-5'\n_____________\|___________________________________________________________\|\n_____________59__________________________________________________________2\n	16 -- 22	52 -- 58	-40.891 kcal/mol	20.495 kcal/mol	12.7026 kcal/mol	15 73@LB@ \| \|@LB@5'-GUG...CGCCU G G A UC G UC UGU AA G CACCG...UCC-3'@LB@ GUUCGAU A GUGGG UA AGG CUGGA GGU GAAUAU ACCUC GUG CCU@LB@ :\|:\|\|\|\| \| \|\|\|:: \|\| \|\|\| \|\|\|:\| \|:\| \|\|\|:\|\| \|\|\|\|\| \|\|: \|\|\|@LB@ UAGGCUA U CACUU AU UCC GACUU CUA CUUGUA UGGAG CAU GGA@LB@3'-AUU...CGGUU A G C UU A U U GAA A G UG-5'@LB@ \| \|@LB@ 59 2@LB@@LB@@LB@Energy -7.72 kcal/mol@LB@Hybridization Energy -40.891 kcal/mol@LB@Unfolding Energy - mRNA 20.495 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 16 -- 72@LB@Position - sRNA 3 -- 58@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 52 -- 58@LB@
117	0.003878	0.1165	b3078	ygjI	-10.25	0.038289	174 -- 181	1 -- 8	putative transporter	b0899	_____________173______182\n_____________\|________\|\n5'-GGA...ACCGC________UCAUU...UUG-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	175 -- 181	1 -- 7	-12.7576 kcal/mol	0.416118 kcal/mol	2.11603 kcal/mol	173 182@LB@ \| \|@LB@5'-GGA...ACCGC UCAUU...UUG-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -12.7576 kcal/mol@LB@Unfolding Energy - mRNA 0.416118 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 174 -- 181@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 1 -- 7@LB@
170	0.007042	0.1457	b3110	yhaO	-10.02	0.044877	174 -- 180	1 -- 7	putative transporter		_____________173_____181\n_____________\|_______\|\n5'-AAU...AAUAA_______AAAAU...UCG-3'\n______________GCCCUAC\n______________:\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	174 -- 180	1 -- 7	-12.6531 kcal/mol	0.621925 kcal/mol	2.03949 kcal/mol	173 181@LB@ \| \|@LB@5'-AAU...AAUAA AAAAU...UCG-3'@LB@ GCCCUAC@LB@ :\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -12.6531 kcal/mol@LB@Unfolding Energy - mRNA 0.621925 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 174 -- 180@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 1 -- 7@LB@
3	0	0	b2564	pdxJ	-5.03	0.588876	273 -- 283	52 -- 62	pyridoxine 5'-phosphate synthase		_____________272_________284\n_____________\|___________\|\n5'-AAA...CUUAC___________GCAGG...UUG-3'\n______________CCGGAUCCGGU\n______________\|\|::\|\|\|\|\|:\|\n______________GGUUUAGGCUA\n3'-AUU...AAGUC___________AUGCA...AUG-5'\n_____________\|___________\|\n_____________63__________51\n	277 -- 283	52 -- 58	-14.6263 kcal/mol	4.30712 kcal/mol	5.31395 kcal/mol	272 284@LB@ \| \|@LB@5'-AAA...CUUAC GCAGG...UUG-3'@LB@ CCGGAUCCGGU@LB@ \|\|::\|\|\|\|\|:\|@LB@ GGUUUAGGCUA@LB@3'-AUU...AAGUC AUGCA...AUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -14.6263 kcal/mol@LB@Unfolding Energy - mRNA 4.30712 kcal/mol@LB@Unfolding Energy - sRNA 5.31395 kcal/mol@LB@@LB@Position - mRNA 273 -- 283@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 52 -- 58@LB@
189	0.008373	0.1558	b1559	quuQ	-11.90	0.011421	197 -- 219	1 -- 24	Qin prophage; putative antitermination protein Q		_____________196______________________220\n_____________\|________________________\|\n5'-UCU...AGAAC______GA______GAA_______CAAAA...AUG-3'\n______________GAGCAU___ACCUU___GCCUUAC\n______________\|\|:\|\|\|___\|\|\|\|:___:\|\|:\|\|\|\n______________CUUGUA___UGGAG___UGGGAUG\n3'-AUU...UCUAU______GAA_____ACA_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	213 -- 219	1 -- 7	-21.9861 kcal/mol	2.0909 kcal/mol	8.02158 kcal/mol	196 220@LB@ \| \|@LB@5'-UCU...AGAAC GA GAA CAAAA...AUG-3'@LB@ GAGCAU ACCUU GCCUUAC@LB@ \|\|:\|\|\| \|\|\|\|: :\|\|:\|\|\|@LB@ CUUGUA UGGAG UGGGAUG@LB@3'-AUU...UCUAU GAA ACA -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -21.9861 kcal/mol@LB@Unfolding Energy - mRNA 2.0909 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 197 -- 219@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 1 -- 7@LB@
93	0.002634	0.09947	b2202	napC	-9.04	0.084220	177 -- 197	34 -- 54	quinol dehydrogenase electron source for NapAB		_____________176___________________198\n_____________\|_____________________\|\n5'-ACG...CAAAA_______G___A_________AUUAU...GUU-3'\n______________GGUUACG_GAA_UAAGAGGUU\n______________\|:\|\|\|\|\|_\|\|\|_\|\|\|:\|\|\|\|:\n______________CUAAUGC_CUU_AUUUUCCAG\n3'-AUU...UUAGG_______A___C_________ACUUU...AUG-5'\n_____________\|_____________________\|\n_____________55____________________33\n	177 -- 183	48 -- 54	-21.2793 kcal/mol	4.43682 kcal/mol	7.71857 kcal/mol	176 198@LB@ \| \|@LB@5'-ACG...CAAAA G A AUUAU...GUU-3'@LB@ GGUUACG GAA UAAGAGGUU@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|:\|\|\|\|:@LB@ CUAAUGC CUU AUUUUCCAG@LB@3'-AUU...UUAGG A C ACUUU...AUG-5'@LB@ \| \|@LB@ 55 33@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -21.2793 kcal/mol@LB@Unfolding Energy - mRNA 4.43682 kcal/mol@LB@Unfolding Energy - sRNA 7.71857 kcal/mol@LB@@LB@Position - mRNA 177 -- 197@LB@Position - sRNA 34 -- 54@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 48 -- 54@LB@
183	0.007903	0.1519	b2725	hycA	-8.51	0.115738	229 -- 236	49 -- 56	regulator of the transcriptional regulator FhlA		_____________228______237\n_____________\|________\|\n5'-UUA...GAAAG________AUCGC...AGG-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	230 -- 236	49 -- 55	-10.9203 kcal/mol	2.09518 kcal/mol	0.317884 kcal/mol	228 237@LB@ \| \|@LB@5'-UUA...GAAAG AUCGC...AGG-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -10.9203 kcal/mol@LB@Unfolding Energy - mRNA 2.09518 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 229 -- 236@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 49 -- 55@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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