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
61	0.01292	0.6177	b4154	frdA	-9.46	0.053105	187 -- 202	38 -- 54	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit	_____________186_______________203\n_____________\|_________________\|\n5'-UAA...AACAA__U_________G____GCAAA...UCG-3'\n______________UC__GGAGGAAU_UCGU\n______________\|\|__:\|\|\|\|\|\|\|_\|\|:\|\n______________AG__UCUCCUUA_AGUA\n3'-UUU...CGGGC__UU________A____AAAAA...ACA-5'\n_____________\|_________________\|\n_____________55________________37\n	191 -- 197	43 -- 49	-14.1575 kcal/mol	3.5319 kcal/mol	1.17036 kcal/mol	186 203@LB@ \| \|@LB@5'-UAA...AACAA U G GCAAA...UCG-3'@LB@ UC GGAGGAAU UCGU@LB@ \|\| :\|\|\|\|\|\|\| \|\|:\|@LB@ AG UCUCCUUA AGUA@LB@3'-UUU...CGGGC UU A AAAAA...ACA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -14.1575 kcal/mol@LB@Unfolding Energy - mRNA 3.5319 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 187 -- 202@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 43 -- 49@LB@
91	0.01869	0.6177	b3432	glgB	-9.43	0.053684	93 -- 103	45 -- 56	1 4-alpha-glucan branching enzyme	_____________92___________104\n_____________\|____________\|\n5'-CAU...GACGA____________UGCAC...GAC-3'\n______________CG_CAGAGAGGA\n______________\|\|_\|\|:\|\|\|\|\|\|\n______________GC_GUUUCUCCU\n3'-UUU...ACCGG__A_________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	97 -- 103	45 -- 51	-14.5586 kcal/mol	4.18817 kcal/mol	0.938337 kcal/mol	92 104@LB@ \| \|@LB@5'-CAU...GACGA UGCAC...GAC-3'@LB@ CG CAGAGAGGA@LB@ \|\| \|\|:\|\|\|\|\|\|@LB@ GC GUUUCUCCU@LB@3'-UUU...ACCGG A UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -14.5586 kcal/mol@LB@Unfolding Energy - mRNA 4.18817 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 93 -- 103@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 45 -- 51@LB@
172	0.03476	0.6177	b3441	yhhY	-9.34	0.055938	185 -- 193	45 -- 53	aminoacyl nucleotide detoxifying acetyltransferase	_____________184_______194\n_____________\|_________\|\n5'-CCC...UACCC_________CAAAG...UGC-3'\n______________CAAAGAGGA\n______________\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	187 -- 193	45 -- 51	-12.8083 kcal/mol	2.54681 kcal/mol	0.917553 kcal/mol	184 194@LB@ \| \|@LB@5'-CCC...UACCC CAAAG...UGC-3'@LB@ CAAAGAGGA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -12.8083 kcal/mol@LB@Unfolding Energy - mRNA 2.54681 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 185 -- 193@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
63	0.01324	0.6177	b3140	agaD	-9.33	0.056359	182 -- 192	45 -- 55	N-acetylgalactosamine-specific enzyme IID component of PTS	_____________181_________193\n_____________\|___________\|\n5'-GCG...AAAAU_AA________CUACA...GUU-3'\n______________G__GAAGAGGA\n______________\|__:\|\|\|\|\|\|\|\n______________C__UUUCUCCU\n3'-UUU...CCGGG_AG________UAAAG...ACA-5'\n_____________\|___________\|\n_____________56__________44\n	186 -- 192	45 -- 51	-11.186 kcal/mol	0.927202 kcal/mol	0.930875 kcal/mol	181 193@LB@ \| \|@LB@5'-GCG...AAAAU AA CUACA...GUU-3'@LB@ G GAAGAGGA@LB@ \| :\|\|\|\|\|\|\|@LB@ C UUUCUCCU@LB@3'-UUU...CCGGG AG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -11.186 kcal/mol@LB@Unfolding Energy - mRNA 0.927202 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 182 -- 192@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 45 -- 51@LB@
57	0.01201	0.6177	b2959	yggL	-9.33	0.056423	82 -- 92	47 -- 57	DUF469 family protein	_____________81__________93\n_____________\|___________\|\n5'-GUA...AAAAC___________CAAUG...CAU-3'\n______________CUGUCAGAGAG\n______________\|:\|\|\|\|:\|\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	86 -- 92	47 -- 53	-15.1623 kcal/mol	3.10124 kcal/mol	2.73556 kcal/mol	81 93@LB@ \| \|@LB@5'-GUA...AAAAC CAAUG...CAU-3'@LB@ CUGUCAGAGAG@LB@ \|:\|\|\|\|:\|\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -15.1623 kcal/mol@LB@Unfolding Energy - mRNA 3.10124 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 82 -- 92@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 47 -- 53@LB@
107	0.02168	0.6177	b1738	chbB	-9.32	0.056668	26 -- 34	47 -- 55	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________25________35\n_____________\|_________\|\n5'-AAU...CACAG_________AAACA...CGG-3'\n______________GUCAAGGAG\n______________\|\|\|\|\|:\|\|\|\n______________CAGUUUCUC\n3'-UUU...CCGGG_________CUUAA...ACA-5'\n_____________\|_________\|\n_____________56________46\n	28 -- 34	47 -- 53	-13.6925 kcal/mol	3.47679 kcal/mol	0.899516 kcal/mol	25 35@LB@ \| \|@LB@5'-AAU...CACAG AAACA...CGG-3'@LB@ GUCAAGGAG@LB@ \|\|\|\|\|:\|\|\|@LB@ CAGUUUCUC@LB@3'-UUU...CCGGG CUUAA...ACA-5'@LB@ \| \|@LB@ 56 46@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -13.6925 kcal/mol@LB@Unfolding Energy - mRNA 3.47679 kcal/mol@LB@Unfolding Energy - sRNA 0.899516 kcal/mol@LB@@LB@Position - mRNA 26 -- 34@LB@Position - sRNA 47 -- 55@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 47 -- 53@LB@
175	0.03585	0.6177	b2028	ugd	-9.30	0.056993	217 -- 248	46 -- 74	UDP-glucose 6-dehydrogenase	_____________216______________________________249\n_____________\|________________________________\|\n5'-GCU...CAUUU______C_G_____GUA___________C___CUUCU...CAC-3'\n______________CCGGUA_U_GCUAU___GGCUUGUCAAA_GGG\n______________\|\|::\|\|_\|_\|\|\|\|\|___\|\|\|::\|\|\|\|\|\|_:\|\|\n______________GGUUAU_A_CGAUA___CCGGGCAGUUU_UCC\n3'-UUU...UUACC________G_____A_____________C___UUAAA...ACA-5'\n_____________\|________________________________\|\n_____________75_______________________________45\n	238 -- 244	50 -- 56	-30.8605 kcal/mol	10.2215 kcal/mol	11.335 kcal/mol	216 249@LB@ \| \|@LB@5'-GCU...CAUUU C G GUA C CUUCU...CAC-3'@LB@ CCGGUA U GCUAU GGCUUGUCAAA GGG@LB@ \|\|::\|\| \| \|\|\|\|\| \|\|\|::\|\|\|\|\|\| :\|\|@LB@ GGUUAU A CGAUA CCGGGCAGUUU UCC@LB@3'-UUU...UUACC G A C UUAAA...ACA-5'@LB@ \| \|@LB@ 75 45@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -30.8605 kcal/mol@LB@Unfolding Energy - mRNA 10.2215 kcal/mol@LB@Unfolding Energy - sRNA 11.335 kcal/mol@LB@@LB@Position - mRNA 217 -- 248@LB@Position - sRNA 46 -- 74@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 50 -- 56@LB@
90	0.01863	0.6177	b0659	ybeY	-9.29	0.057244	42 -- 51	47 -- 56	ssRNA-specific endoribonuclease; 16S rRNA 3' end maturation and quality control co-endoribonuclease working with RNase R; rRNA transcription antitermination factor	_____________41_________52\n_____________\|__________\|\n5'-ACU...GCCGA__________AUCAG...CGC-3'\n______________UGUCGAAGAG\n______________:\|\|\|:\|\|\|\|\|\n______________GCAGUUUCUC\n3'-UUU...ACCGG__________CUUAA...ACA-5'\n_____________\|__________\|\n_____________57_________46\n	45 -- 51	47 -- 53	-13.0692 kcal/mol	2.86289 kcal/mol	0.911734 kcal/mol	41 52@LB@ \| \|@LB@5'-ACU...GCCGA AUCAG...CGC-3'@LB@ UGUCGAAGAG@LB@ :\|\|\|:\|\|\|\|\|@LB@ GCAGUUUCUC@LB@3'-UUU...ACCGG CUUAA...ACA-5'@LB@ \| \|@LB@ 57 46@LB@@LB@@LB@Energy -9.29 kcal/mol@LB@Hybridization Energy -13.0692 kcal/mol@LB@Unfolding Energy - mRNA 2.86289 kcal/mol@LB@Unfolding Energy - sRNA 0.911734 kcal/mol@LB@@LB@Position - mRNA 42 -- 51@LB@Position - sRNA 47 -- 56@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 47 -- 53@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@
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@

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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