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
18	0.003456	0.593	b0867	amiD	-11.23	0.023022	276 -- 289	39 -- 52	1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein	_____________275____________290\n_____________\|______________\|\n5'-GAU...UCGAG__________A___GCUUG...CCC-3'\n______________AAAGAGGGAU_UCA\n______________\|\|\|\|\|\|\|:\|\|_\|\|\|\n______________UUUCUCCUUA_AGU\n3'-UUU...GGCAG__________A___AAAAA...ACA-5'\n_____________\|______________\|\n_____________53_____________38\n	279 -- 285	43 -- 49	-14.4178 kcal/mol	2.13665 kcal/mol	1.05043 kcal/mol	275 290@LB@ \| \|@LB@5'-GAU...UCGAG A GCUUG...CCC-3'@LB@ AAAGAGGGAU UCA@LB@ \|\|\|\|\|\|\|:\|\| \|\|\|@LB@ UUUCUCCUUA AGU@LB@3'-UUU...GGCAG A AAAAA...ACA-5'@LB@ \| \|@LB@ 53 38@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -14.4178 kcal/mol@LB@Unfolding Energy - mRNA 2.13665 kcal/mol@LB@Unfolding Energy - sRNA 1.05043 kcal/mol@LB@@LB@Position - mRNA 276 -- 289@LB@Position - sRNA 39 -- 52@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 43 -- 49@LB@
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@
67	0.01414	0.6177	b0474	adk	-7.17	0.151538	186 -- 198	39 -- 51	adenylate kinase	_____________185___________199\n_____________\|_____________\|\n5'-ACC...AUUUU_______U_____CAAUG...AUA-3'\n______________AAGGGGA_UUUCG\n______________\|\|\|:\|\|\|_\|\|\|\|:\n______________UUCUCCU_AAAGU\n3'-UUU...GCAGU_______U_____AAAAA...ACA-5'\n_____________\|_____________\|\n_____________52____________38\n	186 -- 192	45 -- 51	-12.5937 kcal/mol	4.3836 kcal/mol	1.04441 kcal/mol	185 199@LB@ \| \|@LB@5'-ACC...AUUUU U CAAUG...AUA-3'@LB@ AAGGGGA UUUCG@LB@ \|\|\|:\|\|\| \|\|\|\|:@LB@ UUCUCCU AAAGU@LB@3'-UUU...GCAGU U AAAAA...ACA-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -12.5937 kcal/mol@LB@Unfolding Energy - mRNA 4.3836 kcal/mol@LB@Unfolding Energy - sRNA 1.04441 kcal/mol@LB@@LB@Position - mRNA 186 -- 198@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 45 -- 51@LB@
100	0.01963	0.6177	b4001	yjaH	-9.93	0.042585	215 -- 230	39 -- 53	DUF1481 family putative lipoprotein	_____________214______________231\n_____________\|________________\|\n5'-UGG...UUUAA________U_______CCCCU...AUA-3'\n______________CGAAGGGG_GGUUUCA\n______________\|:\|\|\|:\|\|_::\|\|\|\|\|\n______________GUUUCUCC_UUAAAGU\n3'-UUU...GGGCA________________AAAAA...ACA-5'\n_____________\|________________\|\n_____________54_______________38\n	216 -- 222	46 -- 52	-15.2589 kcal/mol	4.19806 kcal/mol	1.13439 kcal/mol	214 231@LB@ \| \|@LB@5'-UGG...UUUAA U CCCCU...AUA-3'@LB@ CGAAGGGG GGUUUCA@LB@ \|:\|\|\|:\|\| ::\|\|\|\|\|@LB@ GUUUCUCC UUAAAGU@LB@3'-UUU...GGGCA AAAAA...ACA-5'@LB@ \| \|@LB@ 54 38@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -15.2589 kcal/mol@LB@Unfolding Energy - mRNA 4.19806 kcal/mol@LB@Unfolding Energy - sRNA 1.13439 kcal/mol@LB@@LB@Position - mRNA 215 -- 230@LB@Position - sRNA 39 -- 53@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 46 -- 52@LB@
141	0.02753	0.6177	b3215	yhcA	-6.30	0.221284	185 -- 194	39 -- 48	putative periplasmic chaperone protein	_____________184________195\n_____________\|__________\|\n5'-ACG...AUUAC__________AUUUA...AAA-3'\n______________AGGAGUUUUA\n______________\|\|\|\|:\|\|\|:\|\n______________UCCUUAAAGU\n3'-UUU...GUUUC__________AAAAA...ACA-5'\n_____________\|__________\|\n_____________49_________38\n	187 -- 193	40 -- 46	-10.0044 kcal/mol	2.68942 kcal/mol	1.01866 kcal/mol	184 195@LB@ \| \|@LB@5'-ACG...AUUAC AUUUA...AAA-3'@LB@ AGGAGUUUUA@LB@ \|\|\|\|:\|\|\|:\|@LB@ UCCUUAAAGU@LB@3'-UUU...GUUUC AAAAA...ACA-5'@LB@ \| \|@LB@ 49 38@LB@@LB@@LB@Energy -6.30 kcal/mol@LB@Hybridization Energy -10.0044 kcal/mol@LB@Unfolding Energy - mRNA 2.68942 kcal/mol@LB@Unfolding Energy - sRNA 1.01866 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 39 -- 48@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
158	0.03174	0.6177	b3185	rpmA	-9.10	0.062717	186 -- 199	39 -- 52	50S ribosomal subunit protein L27	_____________185____________200\n_____________\|______________\|\n5'-GAA...GACCU______A_______AAUGG...CGG-3'\n______________GAGGAG_GAUUUCA\n______________:\|:\|\|\|_:\|\|\|\|\|\|\n______________UUUCUC_UUAAAGU\n3'-UUU...GGCAG______C_______AAAAA...ACA-5'\n_____________\|______________\|\n_____________53_____________38\n	193 -- 199	39 -- 45	-11.8509 kcal/mol	1.7019 kcal/mol	1.05043 kcal/mol	185 200@LB@ \| \|@LB@5'-GAA...GACCU A AAUGG...CGG-3'@LB@ GAGGAG GAUUUCA@LB@ :\|:\|\|\| :\|\|\|\|\|\|@LB@ UUUCUC UUAAAGU@LB@3'-UUU...GGCAG C AAAAA...ACA-5'@LB@ \| \|@LB@ 53 38@LB@@LB@@LB@Energy -9.10 kcal/mol@LB@Hybridization Energy -11.8509 kcal/mol@LB@Unfolding Energy - mRNA 1.7019 kcal/mol@LB@Unfolding Energy - sRNA 1.05043 kcal/mol@LB@@LB@Position - mRNA 186 -- 199@LB@Position - sRNA 39 -- 52@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 39 -- 45@LB@
182	0.03771	0.6177	b0397	sbcC	-11.00	0.025718	84 -- 100	39 -- 56	exonuclease dsDNA ATP-dependent	_____________83_________________101\n_____________\|__________________\|\n5'-GAA...CUCAG___________UG_____AUCGC...UUG-3'\n______________CGUCGAAGAGG___UUCA\n______________\|\|\|\|:\|\|\|\|\|\|___\|\|\|\|\n______________GCAGUUUCUCC___AAGU\n3'-UUU...ACCGG___________UUA____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	88 -- 94	46 -- 52	-19.0672 kcal/mol	6.9127 kcal/mol	1.15786 kcal/mol	83 101@LB@ \| \|@LB@5'-GAA...CUCAG UG AUCGC...UUG-3'@LB@ CGUCGAAGAGG UUCA@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ GCAGUUUCUCC AAGU@LB@3'-UUU...ACCGG UUA AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -19.0672 kcal/mol@LB@Unfolding Energy - mRNA 6.9127 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 84 -- 100@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 46 -- 52@LB@
184	0.03803	0.6177	b3647	ligB	-3.67	0.590336	72 -- 111	39 -- 67	DNA ligase NAD(+)-dependent	_____________71________________________________________112\n_____________\|_________________________________________\|\n5'-GGC...GCUUC_______U________UUCACUGCAAUA____C__U_____GGAAG...AAA-3'\n______________CGC_AUU_GCCUGUCA____________AAGA_GA_UUUCA\n______________\|\|\|_\|\|\|_\|\|\|:\|\|\|\|____________\|\|\|\|_\|\|_\|\|\|\|\|\n______________GCG_UAA_CGGGCAGU____________UUCU_CU_AAAGU\n3'-UUU...UUAUA___A___C________________________C__U_____AAAAA...ACA-5'\n_____________\|_________________________________________\|\n_____________68________________________________________38\n	80 -- 86	52 -- 58	-24.1741 kcal/mol	6.974 kcal/mol	13.5271 kcal/mol	71 112@LB@ \| \|@LB@5'-GGC...GCUUC U UUCACUGCAAUA C U GGAAG...AAA-3'@LB@ CGC AUU GCCUGUCA AAGA GA UUUCA@LB@ \|\|\| \|\|\| \|\|\|:\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|@LB@ GCG UAA CGGGCAGU UUCU CU AAAGU@LB@3'-UUU...UUAUA A C C U AAAAA...ACA-5'@LB@ \| \|@LB@ 68 38@LB@@LB@@LB@Energy -3.67 kcal/mol@LB@Hybridization Energy -24.1741 kcal/mol@LB@Unfolding Energy - mRNA 6.974 kcal/mol@LB@Unfolding Energy - sRNA 13.5271 kcal/mol@LB@@LB@Position - mRNA 72 -- 111@LB@Position - sRNA 39 -- 67@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 52 -- 58@LB@
49	0.009604	0.6129	b1175	minD	-8.49	0.083180	191 -- 199	40 -- 48	inhibitor of FtsZ ring polymerization; chromosome-membrane tethering protein; membrane ATPase of the MinCDEE system	_____________190_______200\n_____________\|_________\|\n5'-CUG...UAACA_________UAUGG...AAA-3'\n______________AGGAAUUUC\n______________\|\|\|\|\|\|\|\|\|\n______________UCCUUAAAG\n3'-UUU...GUUUC_________UAAAA...ACA-5'\n_____________\|_________\|\n_____________49________39\n	193 -- 199	40 -- 46	-11.0161 kcal/mol	1.62901 kcal/mol	0.898161 kcal/mol	190 200@LB@ \| \|@LB@5'-CUG...UAACA UAUGG...AAA-3'@LB@ AGGAAUUUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCCUUAAAG@LB@3'-UUU...GUUUC UAAAA...ACA-5'@LB@ \| \|@LB@ 49 39@LB@@LB@@LB@Energy -8.49 kcal/mol@LB@Hybridization Energy -11.0161 kcal/mol@LB@Unfolding Energy - mRNA 1.62901 kcal/mol@LB@Unfolding Energy - sRNA 0.898161 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 40 -- 48@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 40 -- 46@LB@
54	0.01118	0.6177	b0127	yadG	-7.27	0.144346	282 -- 299	40 -- 55	putative ABC transporter ATPase	_____________281________________300\n_____________\|__________________\|\n5'-UGU...UGCAG_______C___U______U-3'\n______________GUCGAAG_GGG_GAUUUU\n______________\|\|\|:\|\|\|_:\|\|_:\|\|\|\|:\n______________CAGUUUC_UCC_UUAAAG\n3'-UUU...CCGGG__________________UAAAA...ACA-5'\n_____________\|__________________\|\n_____________56_________________39\n	282 -- 288	49 -- 55	-13.6497 kcal/mol	5.35692 kcal/mol	1.01784 kcal/mol	281 300@LB@ \| \|@LB@5'-UGU...UGCAG C U U-3'@LB@ GUCGAAG GGG GAUUUU@LB@ \|\|\|:\|\|\| :\|\| :\|\|\|\|:@LB@ CAGUUUC UCC UUAAAG@LB@3'-UUU...CCGGG UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -13.6497 kcal/mol@LB@Unfolding Energy - mRNA 5.35692 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 282 -- 299@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 49 -- 55@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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