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
176	0.03596	0.6177	b1747	astA	-4.82	0.399998	129 -- 139	46 -- 56	arginine succinyltransferase	_____________128_________140\n_____________\|___________\|\n5'-GGC...GUCAG__AA_______UGACG...AAG-3'\n______________CG__GAAGAGG\n______________\|\|__:\|\|\|\|\|\|\n______________GC__UUUCUCC\n3'-UUU...ACCGG__AG_______UUAAA...ACA-5'\n_____________\|___________\|\n_____________57__________45\n	133 -- 139	46 -- 52	-9.86744 kcal/mol	4.11365 kcal/mol	0.93204 kcal/mol	128 140@LB@ \| \|@LB@5'-GGC...GUCAG AA UGACG...AAG-3'@LB@ CG GAAGAGG@LB@ \|\| :\|\|\|\|\|\|@LB@ GC UUUCUCC@LB@3'-UUU...ACCGG AG UUAAA...ACA-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -4.82 kcal/mol@LB@Hybridization Energy -9.86744 kcal/mol@LB@Unfolding Energy - mRNA 4.11365 kcal/mol@LB@Unfolding Energy - sRNA 0.93204 kcal/mol@LB@@LB@Position - mRNA 129 -- 139@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 46 -- 52@LB@
39	0.007917	0.6129	b3657	yicJ	-11.19	0.023423	220 -- 230	47 -- 57	putative transporter	_____________219_________231\n_____________\|___________\|\n5'-CAG...GUUGU___________AAAAU...UGU-3'\n______________CCGUUAAAGAG\n______________\|\|\|\|:\|\|\|\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	224 -- 230	47 -- 53	-15.9196 kcal/mol	1.98973 kcal/mol	2.73556 kcal/mol	219 231@LB@ \| \|@LB@5'-CAG...GUUGU AAAAU...UGU-3'@LB@ CCGUUAAAGAG@LB@ \|\|\|\|:\|\|\|\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -15.9196 kcal/mol@LB@Unfolding Energy - mRNA 1.98973 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 220 -- 230@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 47 -- 53@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@
88	0.01799	0.6177	b0415	ribE	-8.66	0.076826	57 -- 64	47 -- 54	riboflavin synthase beta chain	_____________56_______65\n_____________\|________\|\n5'-CGG...UAAAU________AUACG...GUG-3'\n______________UCAAAGAG\n______________\|\|\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	58 -- 64	47 -- 53	-10.4141 kcal/mol	0.855178 kcal/mol	0.897871 kcal/mol	56 65@LB@ \| \|@LB@5'-CGG...UAAAU AUACG...GUG-3'@LB@ UCAAAGAG@LB@ \|\|\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -10.4141 kcal/mol@LB@Unfolding Energy - mRNA 0.855178 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 57 -- 64@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 47 -- 53@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@
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@
108	0.0217	0.6177	b0243	proA	-8.76	0.073409	183 -- 193	47 -- 57	gamma-glutamylphosphate reductase	_____________182_________194\n_____________\|___________\|\n5'-AAU...AUUAC___________CAGGC...AUG-3'\n______________CCGUUAAGGAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	187 -- 193	47 -- 53	-14.7866 kcal/mol	3.29159 kcal/mol	2.73556 kcal/mol	182 194@LB@ \| \|@LB@5'-AAU...AUUAC CAGGC...AUG-3'@LB@ CCGUUAAGGAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -14.7866 kcal/mol@LB@Unfolding Energy - mRNA 3.29159 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 183 -- 193@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 47 -- 53@LB@
114	0.02277	0.6177	b4077	gltP	-4.92	0.386213	48 -- 56	47 -- 55	glutamate/aspartate:proton symporter	_____________47________57\n_____________\|_________\|\n5'-GCC...CUGUU_________UUGCG...GCG-3'\n______________GUUAAAGGG\n______________\|\|:\|\|\|\|:\|\n______________CAGUUUCUC\n3'-UUU...CCGGG_________CUUAA...ACA-5'\n_____________\|_________\|\n_____________56________46\n	50 -- 56	47 -- 53	-9.45392 kcal/mol	3.63887 kcal/mol	0.899516 kcal/mol	47 57@LB@ \| \|@LB@5'-GCC...CUGUU UUGCG...GCG-3'@LB@ GUUAAAGGG@LB@ \|\|:\|\|\|\|:\|@LB@ CAGUUUCUC@LB@3'-UUU...CCGGG CUUAA...ACA-5'@LB@ \| \|@LB@ 56 46@LB@@LB@@LB@Energy -4.92 kcal/mol@LB@Hybridization Energy -9.45392 kcal/mol@LB@Unfolding Energy - mRNA 3.63887 kcal/mol@LB@Unfolding Energy - sRNA 0.899516 kcal/mol@LB@@LB@Position - mRNA 48 -- 56@LB@Position - sRNA 47 -- 55@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 47 -- 53@LB@
116	0.02318	0.6177	b1726	yniB	-7.96	0.105879	188 -- 195	47 -- 54	putative inner membrane protein	_____________187______196\n_____________\|________\|\n5'-AAG...CUUAA________AACUC...UGA-3'\n______________UCAAGGAG\n______________\|\|\|\|:\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	189 -- 195	47 -- 53	-9.99546 kcal/mol	1.13532 kcal/mol	0.897871 kcal/mol	187 196@LB@ \| \|@LB@5'-AAG...CUUAA AACUC...UGA-3'@LB@ UCAAGGAG@LB@ \|\|\|\|:\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -9.99546 kcal/mol@LB@Unfolding Energy - mRNA 1.13532 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 188 -- 195@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 47 -- 53@LB@
121	0.02422	0.6177	b0754	aroG	-7.67	0.121074	238 -- 245	47 -- 54	3-deoxy-D-arabino-heptulosonate-7-phosphate synthase phenylalanine repressible	_____________237______246\n_____________\|________\|\n5'-CUU...AGAAA________UUACU...CGA-3'\n______________UCAAAGAG\n______________\|\|\|\|\|\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	239 -- 245	47 -- 53	-9.80538 kcal/mol	1.24089 kcal/mol	0.897871 kcal/mol	237 246@LB@ \| \|@LB@5'-CUU...AGAAA UUACU...CGA-3'@LB@ UCAAAGAG@LB@ \|\|\|\|\|\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -9.80538 kcal/mol@LB@Unfolding Energy - mRNA 1.24089 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 238 -- 245@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 239 -- 245@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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service.

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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