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
181	0.03769	0.6177	b0912	ihfB	-7.34	0.140491	192 -- 199	43 -- 50	integration host factor (IHF) DNA-binding protein beta subunit	_____________191______200\n_____________\|________\|\n5'-ACG...GAACC________CAUGA...UGG-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	193 -- 199	43 -- 49	-10.3812 kcal/mol	2.20002 kcal/mol	0.845564 kcal/mol	191 200@LB@ \| \|@LB@5'-ACG...GAACC CAUGA...UGG-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -7.34 kcal/mol@LB@Hybridization Energy -10.3812 kcal/mol@LB@Unfolding Energy - mRNA 2.20002 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 192 -- 199@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 43 -- 49@LB@
137	0.02646	0.6177	b3807	cyaY	-4.99	0.375460	213 -- 221	38 -- 46	iron-dependent inhibitor of iron-sulfur cluster formation; frataxin; iron-binding and oxidizing protein	_____________212_______222\n_____________\|_________\|\n5'-UGA...ACAGU_________CGCCU...AAA-3'\n______________GAAUUUCAU\n______________\|\|\|\|\|\|\|\|\|\n______________CUUAAAGUA\n3'-UUU...UUCUC_________AAAAA...ACA-5'\n_____________\|_________\|\n_____________47________37\n	215 -- 221	38 -- 44	-7.89908 kcal/mol	1.90809 kcal/mol	1.00074 kcal/mol	212 222@LB@ \| \|@LB@5'-UGA...ACAGU CGCCU...AAA-3'@LB@ GAAUUUCAU@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUUAAAGUA@LB@3'-UUU...UUCUC AAAAA...ACA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -4.99 kcal/mol@LB@Hybridization Energy -7.89908 kcal/mol@LB@Unfolding Energy - mRNA 1.90809 kcal/mol@LB@Unfolding Energy - sRNA 1.00074 kcal/mol@LB@@LB@Position - mRNA 213 -- 221@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 38 -- 44@LB@
186	0.03879	0.6177	b2898	ygfZ	-4.98	0.377094	224 -- 230	51 -- 57	iron-sulfur cluster repair protein plumbagin resistance	_____________223_____231\n_____________\|_______\|\n5'-CGU...CCUCC_______CCUAC...CUG-3'\n______________CCGUCAG\n______________\|\|\|\|\|\|:\n______________GGCAGUU\n3'-UUU...AACCG_______UCUCC...ACA-5'\n_____________\|_______\|\n_____________58______50\n	224 -- 230	51 -- 57	-9.02345 kcal/mol	1.32881 kcal/mol	2.71582 kcal/mol	223 231@LB@ \| \|@LB@5'-CGU...CCUCC CCUAC...CUG-3'@LB@ CCGUCAG@LB@ \|\|\|\|\|\|:@LB@ GGCAGUU@LB@3'-UUU...AACCG UCUCC...ACA-5'@LB@ \| \|@LB@ 58 50@LB@@LB@@LB@Energy -4.98 kcal/mol@LB@Hybridization Energy -9.02345 kcal/mol@LB@Unfolding Energy - mRNA 1.32881 kcal/mol@LB@Unfolding Energy - sRNA 2.71582 kcal/mol@LB@@LB@Position - mRNA 224 -- 230@LB@Position - sRNA 51 -- 57@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 51 -- 57@LB@
180	0.03697	0.6177	b1325	ycjG	-6.24	0.226397	189 -- 195	47 -- 53	L-Ala-D/L-Glu epimerase	_____________188_____196\n_____________\|_______\|\n5'-AAG...GACAA_______UAAAG...AAC-3'\n______________CAAGGAG\n______________\|\|\|:\|\|\|\n______________GUUUCUC\n3'-UUU...GGGCA_______CUUAA...ACA-5'\n_____________\|_______\|\n_____________54______46\n	189 -- 195	47 -- 53	-8.11062 kcal/mol	0.981925 kcal/mol	0.886139 kcal/mol	188 196@LB@ \| \|@LB@5'-AAG...GACAA UAAAG...AAC-3'@LB@ CAAGGAG@LB@ \|\|\|:\|\|\|@LB@ GUUUCUC@LB@3'-UUU...GGGCA CUUAA...ACA-5'@LB@ \| \|@LB@ 54 46@LB@@LB@@LB@Energy -6.24 kcal/mol@LB@Hybridization Energy -8.11062 kcal/mol@LB@Unfolding Energy - mRNA 0.981925 kcal/mol@LB@Unfolding Energy - sRNA 0.886139 kcal/mol@LB@@LB@Position - mRNA 189 -- 195@LB@Position - sRNA 47 -- 53@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 47 -- 53@LB@
58	0.01235	0.6177	b3903	rhaA	-9.27	0.057813	267 -- 276	46 -- 55	L-rhamnose isomerase	_____________266________277\n_____________\|__________\|\n5'-GCC...UUGAU__________CGCUG...UAC-3'\n______________GUCGAGGAGG\n______________\|\|\|:\|:\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	270 -- 276	46 -- 52	-15.3197 kcal/mol	5.12197 kcal/mol	0.924411 kcal/mol	266 277@LB@ \| \|@LB@5'-GCC...UUGAU CGCUG...UAC-3'@LB@ GUCGAGGAGG@LB@ \|\|\|:\|:\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -15.3197 kcal/mol@LB@Unfolding Energy - mRNA 5.12197 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 267 -- 276@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 46 -- 52@LB@
183	0.03803	0.6177	b3616	tdh	-7.63	0.122830	33 -- 50	37 -- 52	L-threonine 3-dehydrogenase NAD(P)-binding	_____________32_________________51\n_____________\|__________________\|\n5'-UAG...UGCAA________C____A____ACCGG...GUA-3'\n______________AAAGAGGG_AUUU_CGUU\n______________\|\|\|\|\|\|\|:_\|\|\|\|_\|:\|\|\n______________UUUCUCCU_UAAA_GUAA\n3'-UUU...GGCAG__________________AAAAA...ACA-5'\n_____________\|__________________\|\n_____________53_________________36\n	34 -- 40	45 -- 51	-11.8553 kcal/mol	3.14412 kcal/mol	1.07641 kcal/mol	32 51@LB@ \| \|@LB@5'-UAG...UGCAA C A ACCGG...GUA-3'@LB@ AAAGAGGG AUUU CGUU@LB@ \|\|\|\|\|\|\|: \|\|\|\| \|:\|\|@LB@ UUUCUCCU UAAA GUAA@LB@3'-UUU...GGCAG AAAAA...ACA-5'@LB@ \| \|@LB@ 53 36@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -11.8553 kcal/mol@LB@Unfolding Energy - mRNA 3.14412 kcal/mol@LB@Unfolding Energy - sRNA 1.07641 kcal/mol@LB@@LB@Position - mRNA 33 -- 50@LB@Position - sRNA 37 -- 52@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 45 -- 51@LB@
113	0.02257	0.6177	b0915	lpxK	-7.55	0.127690	105 -- 116	46 -- 56	lipid A 4'kinase	_____________104__________117\n_____________\|____________\|\n5'-GAA...GUGGU_________U__UGUCA...GCU-3'\n______________CGUCGAGGA_GG\n______________\|\|\|\|:\|:\|\|_\|\|\n______________GCAGUUUCU_CC\n3'-UUU...ACCGG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________57___________45\n	107 -- 113	48 -- 54	-12.734 kcal/mol	4.25329 kcal/mol	0.93204 kcal/mol	104 117@LB@ \| \|@LB@5'-GAA...GUGGU U UGUCA...GCU-3'@LB@ CGUCGAGGA GG@LB@ \|\|\|\|:\|:\|\| \|\|@LB@ GCAGUUUCU CC@LB@3'-UUU...ACCGG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -7.55 kcal/mol@LB@Hybridization Energy -12.734 kcal/mol@LB@Unfolding Energy - mRNA 4.25329 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 105 -- 116@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 48 -- 54@LB@
122	0.02427	0.6177	b1116	lolC	-7.56	0.127136	206 -- 233	55 -- 74	lipoprotein-releasing system transmembrane protein	_____________205__________________________234\n_____________\|____________________________\|\n5'-GUA...AUGUA____CC_______CUAUUU_________CGUUA...GCA-3'\n______________CCAA__UGUCGCU______AUUGGCCUG\n______________\|\|\|\|__\|:\|\|\|\|\|______\|\|\|\|\|\|\|:\|\n______________GGUU__AUAGCGA______UAACCGGGC\n3'-UUU...UUACC____________________________AGUUU...ACA-5'\n_____________\|____________________________\|\n_____________75___________________________54\n	212 -- 218	64 -- 70	-24.394 kcal/mol	5.52374 kcal/mol	11.3119 kcal/mol	205 234@LB@ \| \|@LB@5'-GUA...AUGUA CC CUAUUU CGUUA...GCA-3'@LB@ CCAA UGUCGCU AUUGGCCUG@LB@ \|\|\|\| \|:\|\|\|\|\| \|\|\|\|\|\|\|:\|@LB@ GGUU AUAGCGA UAACCGGGC@LB@3'-UUU...UUACC AGUUU...ACA-5'@LB@ \| \|@LB@ 75 54@LB@@LB@@LB@Energy -7.56 kcal/mol@LB@Hybridization Energy -24.394 kcal/mol@LB@Unfolding Energy - mRNA 5.52374 kcal/mol@LB@Unfolding Energy - sRNA 11.3119 kcal/mol@LB@@LB@Position - mRNA 206 -- 233@LB@Position - sRNA 55 -- 74@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 64 -- 70@LB@
187	0.03882	0.6177	b0403	malZ	-7.79	0.114240	189 -- 197	42 -- 50	maltodextrin glucosidase	_____________188_______198\n_____________\|_________\|\n5'-UUU...AUCAC_________AUGAU...AGC-3'\n______________AGGGGAAUU\n______________\|\|:\|\|\|\|\|\|\n______________UCUCCUUAA\n3'-UUU...CAGUU_________AGUAA...ACA-5'\n_____________\|_________\|\n_____________51________41\n	191 -- 197	42 -- 48	-10.7884 kcal/mol	2.13721 kcal/mol	0.856185 kcal/mol	188 198@LB@ \| \|@LB@5'-UUU...AUCAC AUGAU...AGC-3'@LB@ AGGGGAAUU@LB@ \|\|:\|\|\|\|\|\|@LB@ UCUCCUUAA@LB@3'-UUU...CAGUU AGUAA...ACA-5'@LB@ \| \|@LB@ 51 41@LB@@LB@@LB@Energy -7.79 kcal/mol@LB@Hybridization Energy -10.7884 kcal/mol@LB@Unfolding Energy - mRNA 2.13721 kcal/mol@LB@Unfolding Energy - sRNA 0.856185 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 42 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 42 -- 48@LB@
166	0.03384	0.6177	b4035	malK	-4.35	0.473183	186 -- 196	44 -- 53	maltose ABC transportor ATPase	_____________185_________197\n_____________\|___________\|\n5'-CGC...UGUUA_______A___GGGCA...UGU-3'\n______________CAAAGGG_GAA\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUUUCUC_CUU\n3'-UUU...GGGCA___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________54__________43\n	186 -- 192	47 -- 53	-9.12531 kcal/mol	3.84302 kcal/mol	0.927997 kcal/mol	185 197@LB@ \| \|@LB@5'-CGC...UGUUA A GGGCA...UGU-3'@LB@ CAAAGGG GAA@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUUUCUC CUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -9.12531 kcal/mol@LB@Unfolding Energy - mRNA 3.84302 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 186 -- 196@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 47 -- 53@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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