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
23	0.004411	0.5992	b3390	aroK	-10.22	0.037117	283 -- 298	39 -- 54	shikimate kinase I	_____________282______________299\n_____________\|________________\|\n5'-UGG...ACAAC____UAU_________CG-3'\n______________UCAA___GGAAUUUUA\n______________\|\|\|\|___\|\|\|\|\|\|\|:\|\n______________AGUU___CCUUAAAGU\n3'-UUU...CGGGC____UCU_________AAAAA...ACA-5'\n_____________\|________________\|\n_____________55_______________38\n	292 -- 298	39 -- 45	-11.8677 kcal/mol	0.499768 kcal/mol	1.1491 kcal/mol	282 299@LB@ \| \|@LB@5'-UGG...ACAAC UAU CG-3'@LB@ UCAA GGAAUUUUA@LB@ \|\|\|\| \|\|\|\|\|\|\|:\|@LB@ AGUU CCUUAAAGU@LB@3'-UUU...CGGGC UCU AAAAA...ACA-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -11.8677 kcal/mol@LB@Unfolding Energy - mRNA 0.499768 kcal/mol@LB@Unfolding Energy - sRNA 1.1491 kcal/mol@LB@@LB@Position - mRNA 283 -- 298@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 39 -- 45@LB@
59	0.01284	0.6177	b3453	ugpB	-7.80	0.113752	247 -- 260	43 -- 56	sn-glycerol-3-phosphate ABC transporter periplasmic binding protein	_____________246____________261\n_____________\|______________\|\n5'-UUC...ACUGG______U_______GCACA...UGG-3'\n______________CGUUAA_GGGGAAU\n______________\|\|\|:\|\|_\|:\|\|\|\|\|\n______________GCAGUU_CUCCUUA\n3'-UUU...ACCGG______U_______AAGUA...ACA-5'\n_____________\|______________\|\n_____________57_____________42\n	254 -- 260	43 -- 49	-14.4117 kcal/mol	5.65325 kcal/mol	0.953958 kcal/mol	246 261@LB@ \| \|@LB@5'-UUC...ACUGG U GCACA...UGG-3'@LB@ CGUUAA GGGGAAU@LB@ \|\|\|:\|\| \|:\|\|\|\|\|@LB@ GCAGUU CUCCUUA@LB@3'-UUU...ACCGG U AAGUA...ACA-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -14.4117 kcal/mol@LB@Unfolding Energy - mRNA 5.65325 kcal/mol@LB@Unfolding Energy - sRNA 0.953958 kcal/mol@LB@@LB@Position - mRNA 247 -- 260@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 43 -- 49@LB@
98	0.0193	0.6177	b2705	srlD	-10.75	0.028892	101 -- 114	40 -- 53	sorbitol-6-phosphate dehydrogenase	_____________100____________115\n_____________\|______________\|\n5'-CAC...UUAAA_____C________CGGGC...AUA-3'\n______________CGAAG_GGAAUUUC\n______________\|:\|\|\|_\|\|\|\|\|\|\|\|\n______________GUUUC_CCUUAAAG\n3'-UUU...GGGCA_____U________UAAAA...ACA-5'\n_____________\|______________\|\n_____________54_____________39\n	108 -- 114	40 -- 46	-15.1517 kcal/mol	3.39572 kcal/mol	1.00568 kcal/mol	100 115@LB@ \| \|@LB@5'-CAC...UUAAA C CGGGC...AUA-3'@LB@ CGAAG GGAAUUUC@LB@ \|:\|\|\| \|\|\|\|\|\|\|\|@LB@ GUUUC CCUUAAAG@LB@3'-UUU...GGGCA U UAAAA...ACA-5'@LB@ \| \|@LB@ 54 39@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -15.1517 kcal/mol@LB@Unfolding Energy - mRNA 3.39572 kcal/mol@LB@Unfolding Energy - sRNA 1.00568 kcal/mol@LB@@LB@Position - mRNA 101 -- 114@LB@Position - sRNA 40 -- 53@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 40 -- 46@LB@
161	0.03295	0.6177	b1630	rsxD	-5.86	0.265655	34 -- 42	49 -- 57	SoxR iron-sulfur cluster reduction factor component; putative membrane protein of electron transport complex	_____________33________43\n_____________\|_________\|\n5'-AGC...AGCUG_________CGGCU...CAG-3'\n______________CCGUCGAAG\n______________\|\|\|\|\|:\|\|\|\n______________GGCAGUUUC\n3'-UUU...AACCG_________UCCUU...ACA-5'\n_____________\|_________\|\n_____________58________48\n	36 -- 42	49 -- 55	-12.0908 kcal/mol	3.50131 kcal/mol	2.72876 kcal/mol	33 43@LB@ \| \|@LB@5'-AGC...AGCUG CGGCU...CAG-3'@LB@ CCGUCGAAG@LB@ \|\|\|\|\|:\|\|\|@LB@ GGCAGUUUC@LB@3'-UUU...AACCG UCCUU...ACA-5'@LB@ \| \|@LB@ 58 48@LB@@LB@@LB@Energy -5.86 kcal/mol@LB@Hybridization Energy -12.0908 kcal/mol@LB@Unfolding Energy - mRNA 3.50131 kcal/mol@LB@Unfolding Energy - sRNA 2.72876 kcal/mol@LB@@LB@Position - mRNA 34 -- 42@LB@Position - sRNA 49 -- 57@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 49 -- 55@LB@
134	0.02619	0.6177	b1126	potA	-9.47	0.052791	285 -- 299	37 -- 55	spermidine/putrescine ABC transporter ATPase	_____________284_________________300\n_____________\|___________________\|\n5'-CAA...UUGAU_GU________________C-3'\n______________G__AAAGAGG____UCAUU\n______________\|__\|\|\|\|\|\|\|____\|\|\|\|\|\n______________C__UUUCUCC____AGUAA\n3'-UUU...CCGGG_AG_______UUAA_____AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________36\n	288 -- 294	46 -- 52	-11.4861 kcal/mol	0.840334 kcal/mol	1.17789 kcal/mol	284 300@LB@ \| \|@LB@5'-CAA...UUGAU GU C-3'@LB@ G AAAGAGG UCAUU@LB@ \| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ C UUUCUCC AGUAA@LB@3'-UUU...CCGGG AG UUAA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 36@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -11.4861 kcal/mol@LB@Unfolding Energy - mRNA 0.840334 kcal/mol@LB@Unfolding Energy - sRNA 1.17789 kcal/mol@LB@@LB@Position - mRNA 285 -- 299@LB@Position - sRNA 37 -- 55@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 46 -- 52@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@
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@
27	0.005027	0.5992	b3745	viaA	-10.46	0.033099	243 -- 253	42 -- 52	stimulator of RavA ATPase activity; von Willebrand factor domain protein	_____________242_________254\n_____________\|___________\|\n5'-ACG...UCAGC___________GAUCG...CGG-3'\n______________GAAGAGGGAUU\n______________:\|\|\|\|\|\|:\|\|\|\n______________UUUCUCCUUAA\n3'-UUU...GGCAG___________AGUAA...ACA-5'\n_____________\|___________\|\n_____________53__________41\n	247 -- 253	42 -- 48	-12.7293 kcal/mol	1.40033 kcal/mol	0.866923 kcal/mol	242 254@LB@ \| \|@LB@5'-ACG...UCAGC GAUCG...CGG-3'@LB@ GAAGAGGGAUU@LB@ :\|\|\|\|\|\|:\|\|\|@LB@ UUUCUCCUUAA@LB@3'-UUU...GGCAG AGUAA...ACA-5'@LB@ \| \|@LB@ 53 41@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -12.7293 kcal/mol@LB@Unfolding Energy - mRNA 1.40033 kcal/mol@LB@Unfolding Energy - sRNA 0.866923 kcal/mol@LB@@LB@Position - mRNA 243 -- 253@LB@Position - sRNA 42 -- 52@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 42 -- 48@LB@
96	0.01897	0.6177	b2422	cysA	-7.76	0.115977	190 -- 202	38 -- 50	sulfate/thiosulfate transporter subunit	_____________189___________203\n_____________\|_____________\|\n5'-GGU...CAGCA_______CA____GAGCA...UGC-3'\n______________GGAGGAA__UCAU\n______________:\|\|\|\|\|\|__\|\|\|\|\n______________UCUCCUU__AGUA\n3'-UUU...CAGUU_______AA____AAAAA...ACA-5'\n_____________\|_____________\|\n_____________51____________37\n	190 -- 196	44 -- 50	-11.8687 kcal/mol	3.04673 kcal/mol	1.0603 kcal/mol	189 203@LB@ \| \|@LB@5'-GGU...CAGCA CA GAGCA...UGC-3'@LB@ GGAGGAA UCAU@LB@ :\|\|\|\|\|\| \|\|\|\|@LB@ UCUCCUU AGUA@LB@3'-UUU...CAGUU AA AAAAA...ACA-5'@LB@ \| \|@LB@ 51 37@LB@@LB@@LB@Energy -7.76 kcal/mol@LB@Hybridization Energy -11.8687 kcal/mol@LB@Unfolding Energy - mRNA 3.04673 kcal/mol@LB@Unfolding Energy - sRNA 1.0603 kcal/mol@LB@@LB@Position - mRNA 190 -- 202@LB@Position - sRNA 38 -- 50@LB@Position Seed - mRNA 190 -- 196@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@

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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