Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
71	0.01472	0.6177	b0846	rcdA	-10.28	0.035999	187 -- 195	44 -- 52	transcriptional regulator of csgD and ybiJI; autoregulator	_____________186_______196\n_____________\|_________\|\n5'-GCG...UGCAG_________AUGAC...AAA-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-11.6116 kcal/mol	0.46711 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-GCG...UGCAG AUGAC...AAA-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -11.6116 kcal/mol@LB@Unfolding Energy - mRNA 0.46711 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
72	0.015	0.6177	b2513	yfgM	-10.40	0.034106	179 -- 190	45 -- 55	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________178__________191\n_____________\|____________\|\n5'-GGC...ACUGG________A___GAAGG...UUG-3'\n______________GUUAAGGA_GGA\n______________\|\|:\|\|:\|\|_\|\|\|\n______________CAGUUUCU_CCU\n3'-UUU...CCGGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________56___________44\n	180 -- 186	48 -- 54	-12.2699 kcal/mol	0.940443 kcal/mol	0.930875 kcal/mol	178 191@LB@ \| \|@LB@5'-GGC...ACUGG A GAAGG...UUG-3'@LB@ GUUAAGGA GGA@LB@ \|\|:\|\|:\|\| \|\|\|@LB@ CAGUUUCU CCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -10.40 kcal/mol@LB@Hybridization Energy -12.2699 kcal/mol@LB@Unfolding Energy - mRNA 0.940443 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 179 -- 190@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 48 -- 54@LB@
73	0.01516	0.6177	b0619	citA	-15.44	0.003129	164 -- 175	46 -- 57	sensory histidine kinase in two-component regulatory system with CitB	_____________163__________176\n_____________\|____________\|\n5'-CAU...UACAU____________CUCGG...UCA-3'\n______________CCGUCAAAGAGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GGCAGUUUCUCC\n3'-UUU...AACCG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	169 -- 175	46 -- 52	-20.3901 kcal/mol	2.21322 kcal/mol	2.7365 kcal/mol	163 176@LB@ \| \|@LB@5'-CAU...UACAU CUCGG...UCA-3'@LB@ CCGUCAAAGAGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GGCAGUUUCUCC@LB@3'-UUU...AACCG UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -15.44 kcal/mol@LB@Hybridization Energy -20.3901 kcal/mol@LB@Unfolding Energy - mRNA 2.21322 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 164 -- 175@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 46 -- 52@LB@
74	0.01569	0.6177	b3012	dkgA	-8.72	0.074604	189 -- 197	44 -- 52	2 5-diketo-D-gluconate reductase A	_____________188_______198\n_____________\|_________\|\n5'-CUG...AUAUA_________CGUAU...CCA-3'\n______________AAGGAGGAA\n______________\|\|:\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	191 -- 197	44 -- 50	-11.1725 kcal/mol	1.58724 kcal/mol	0.860683 kcal/mol	188 198@LB@ \| \|@LB@5'-CUG...AUAUA CGUAU...CCA-3'@LB@ AAGGAGGAA@LB@ \|\|:\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.1725 kcal/mol@LB@Unfolding Energy - mRNA 1.58724 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
75	0.01577	0.6177	b1345	intR	-9.71	0.047033	139 -- 151	42 -- 53	Rac prophage; integrase	_____________138___________152\n_____________\|_____________\|\n5'-UAA...GACAG____C________AUCUG...GGG-3'\n______________CAAA_GAGGGAUU\n______________\|\|\|\|_\|\|\|\|:\|\|\|\n______________GUUU_CUCCUUAA\n3'-UUU...GGGCA_____________AGUAA...ACA-5'\n_____________\|_____________\|\n_____________54____________41\n	145 -- 151	42 -- 48	-12.4741 kcal/mol	1.8255 kcal/mol	0.933904 kcal/mol	138 152@LB@ \| \|@LB@5'-UAA...GACAG C AUCUG...GGG-3'@LB@ CAAA GAGGGAUU@LB@ \|\|\|\| \|\|\|\|:\|\|\|@LB@ GUUU CUCCUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -12.4741 kcal/mol@LB@Unfolding Energy - mRNA 1.8255 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 139 -- 151@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 42 -- 48@LB@
76	0.01599	0.6177	b1849	purT	-9.18	0.060248	187 -- 212	25 -- 50	phosphoribosylglycinamide formyltransferase 2	_____________186________________________213\n_____________\|__________________________\|\n5'-UUU...UAAUC______UA______AUGAC_______GGCAC...GUC-3'\n______________AGGGGA__UUCGUU_____GUUAUUA\n______________\|\|:\|\|\|__\|\|\|:\|\|_____:\|\|\|\|\|\|\n______________UCUCCU__AAGUAA_____UAAUAAU\n3'-UUU...CAGUU______UA______AAAAA_______ACGGC...ACA-5'\n_____________\|__________________________\|\n_____________51_________________________24\n	206 -- 212	25 -- 31	-15.1619 kcal/mol	4.88468 kcal/mol	1.09239 kcal/mol	186 213@LB@ \| \|@LB@5'-UUU...UAAUC UA AUGAC GGCAC...GUC-3'@LB@ AGGGGA UUCGUU GUUAUUA@LB@ \|\|:\|\|\| \|\|\|:\|\| :\|\|\|\|\|\|@LB@ UCUCCU AAGUAA UAAUAAU@LB@3'-UUU...CAGUU UA AAAAA ACGGC...ACA-5'@LB@ \| \|@LB@ 51 24@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -15.1619 kcal/mol@LB@Unfolding Energy - mRNA 4.88468 kcal/mol@LB@Unfolding Energy - sRNA 1.09239 kcal/mol@LB@@LB@Position - mRNA 187 -- 212@LB@Position - sRNA 25 -- 50@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 25 -- 31@LB@
77	0.01626	0.6177	b1414	ydcF	-7.59	0.125301	189 -- 198	44 -- 53	DUF218 superfamily protein SAM-binding	_____________188________199\n_____________\|__________\|\n5'-GGU...AACGA__________CCAUG...UGC-3'\n______________UAAGGAGGAA\n______________:\|\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	192 -- 198	44 -- 50	-11.4771 kcal/mol	2.95852 kcal/mol	0.927997 kcal/mol	188 199@LB@ \| \|@LB@5'-GGU...AACGA CCAUG...UGC-3'@LB@ UAAGGAGGAA@LB@ :\|\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -7.59 kcal/mol@LB@Hybridization Energy -11.4771 kcal/mol@LB@Unfolding Energy - mRNA 2.95852 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 189 -- 198@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 44 -- 50@LB@
78	0.01669	0.6177	b2764	cysJ	-9.29	0.057302	85 -- 99	53 -- 70	sulfite reductase alpha subunit flavoprotein	_____________84_________________100\n_____________\|__________________\|\n5'-UUC...UUAGU__________________UUUAA...UUG-3'\n______________UAUCGCUAU___CCCGUC\n______________\|\|\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________AUAGCGAUA___GGGCAG\n3'-UUU...CGGUU_________ACC______UUUCU...ACA-5'\n_____________\|__________________\|\n_____________71_________________52\n	87 -- 93	62 -- 68	-22.2411 kcal/mol	2.01357 kcal/mol	10.9351 kcal/mol	84 100@LB@ \| \|@LB@5'-UUC...UUAGU UUUAA...UUG-3'@LB@ UAUCGCUAU CCCGUC@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ AUAGCGAUA GGGCAG@LB@3'-UUU...CGGUU ACC UUUCU...ACA-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -9.29 kcal/mol@LB@Hybridization Energy -22.2411 kcal/mol@LB@Unfolding Energy - mRNA 2.01357 kcal/mol@LB@Unfolding Energy - sRNA 10.9351 kcal/mol@LB@@LB@Position - mRNA 85 -- 99@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 62 -- 68@LB@
79	0.01695	0.6177	b0435	bolA	-9.02	0.064980	184 -- 202	38 -- 55	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________183_________________203\n_____________\|___________________\|\n5'-UGA...GCGUU___G______AU_______GAUGA...CCG-3'\n______________GUC_GAGGAG__AUUUCAU\n______________\|\|\|_:\|:\|\|\|__\|\|\|\|\|\|\|\n______________CAG_UUUCUC__UAAAGUA\n3'-UUU...CCGGG__________CU_______AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	196 -- 202	38 -- 44	-15.2358 kcal/mol	5.04311 kcal/mol	1.17036 kcal/mol	183 203@LB@ \| \|@LB@5'-UGA...GCGUU G AU GAUGA...CCG-3'@LB@ GUC GAGGAG AUUUCAU@LB@ \|\|\| :\|:\|\|\| \|\|\|\|\|\|\|@LB@ CAG UUUCUC UAAAGUA@LB@3'-UUU...CCGGG CU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.2358 kcal/mol@LB@Unfolding Energy - mRNA 5.04311 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
80	0.01709	0.6177	b2498	upp	-4.70	0.418803	173 -- 195	44 -- 70	uracil phosphoribosyltransferase	_____________172_________________________196\n_____________\|___________________________\|\n5'-GGC...UUUUU___G___________C_______A___AGAGU...CCG-3'\n______________UGU_GCU____GCCC_UCAAAGG_GAA\n______________\|:\|_\|\|\|____\|\|\|\|_\|\|\|\|\|\|:_\|\|\|\n______________AUA_CGA____CGGG_AGUUUCU_CUU\n3'-UUU...CGGUU___G___UAAC____C_______C___AAAGU...ACA-5'\n_____________\|___________________________\|\n_____________71__________________________43\n	185 -- 191	48 -- 54	-22.3772 kcal/mol	6.37003 kcal/mol	11.3101 kcal/mol	172 196@LB@ \| \|@LB@5'-GGC...UUUUU G C A AGAGU...CCG-3'@LB@ UGU GCU GCCC UCAAAGG GAA@LB@ \|:\| \|\|\| \|\|\|\| \|\|\|\|\|\|: \|\|\|@LB@ AUA CGA CGGG AGUUUCU CUU@LB@3'-UUU...CGGUU G UAAC C C AAAGU...ACA-5'@LB@ \| \|@LB@ 71 43@LB@@LB@@LB@Energy -4.70 kcal/mol@LB@Hybridization Energy -22.3772 kcal/mol@LB@Unfolding Energy - mRNA 6.37003 kcal/mol@LB@Unfolding Energy - sRNA 11.3101 kcal/mol@LB@@LB@Position - mRNA 173 -- 195@LB@Position - sRNA 44 -- 70@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 48 -- 54@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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