Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
71	0.01305	0.5385	b3843	ubiD	-10.23	0.096580	123 -- 132	80 -- 89	3-octaprenyl-4-hydroxybenzoate decarboxylase	_____________122________133\n_____________\|__________\|\n5'-CGC...CCGUC__________CUAAU...UGG-3'\n______________AGAGUUCACG\n______________\|:\|\|\|\|\|\|\|\|\n______________UUUCAAGUGC\n3'-CGC...GGCGU__________AACCG...AAG-5'\n_____________\|__________\|\n_____________90_________79\n	126 -- 132	80 -- 86	-13.04 kcal/mol	2.30553 kcal/mol	0.506316 kcal/mol	122 133@LB@ \| \|@LB@5'-CGC...CCGUC CUAAU...UGG-3'@LB@ AGAGUUCACG@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUUCAAGUGC@LB@3'-CGC...GGCGU AACCG...AAG-5'@LB@ \| \|@LB@ 90 79@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -13.04 kcal/mol@LB@Unfolding Energy - mRNA 2.30553 kcal/mol@LB@Unfolding Energy - sRNA 0.506316 kcal/mol@LB@@LB@Position - mRNA 123 -- 132@LB@Position - sRNA 80 -- 89@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 80 -- 86@LB@
72	0.0135	0.5385	b1117	lolD	-8.66	0.177865	184 -- 202	66 -- 83	outer membrane-specific lipoprotein transporter subunit	_____________183_________________203\n_____________\|___________________\|\n5'-GCU...CAACC___UGA_______C_____GAAUA...GCG-3'\n______________CGC___GGCUUUA_GUUAU\n______________\|:\|___\|\|\|\|\|\|\|_\|\|\|\|\|\n______________GUG___CCGAAAU_CAAUA\n3'-CGC...UUCAA___CAA_____________AGCUC...AAG-5'\n_____________\|___________________\|\n_____________84__________________65\n	190 -- 196	71 -- 77	-15.2298 kcal/mol	6.00943 kcal/mol	0.556032 kcal/mol	183 203@LB@ \| \|@LB@5'-GCU...CAACC UGA C GAAUA...GCG-3'@LB@ CGC GGCUUUA GUUAU@LB@ \|:\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ GUG CCGAAAU CAAUA@LB@3'-CGC...UUCAA CAA AGCUC...AAG-5'@LB@ \| \|@LB@ 84 65@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -15.2298 kcal/mol@LB@Unfolding Energy - mRNA 6.00943 kcal/mol@LB@Unfolding Energy - sRNA 0.556032 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 66 -- 83@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 71 -- 77@LB@
73	0.0135	0.5385	b3362	yhfG	-12.23	0.043008	184 -- 212	50 -- 86	putative antitoxin for Fic	_____________183___________________________________213\n_____________\|_____________________________________\|\n5'-GAU...GACAC_____G_GA___A__________A___GA________ACCGA...CUU-3'\n______________GUUCA_G__GGC_________UC_AGU__AGAAACUC\n______________\|\|\|\|\|_\|__\|\|\|_________\|\|_\|\|\|__\|\|\|\|\|\|\|\|\n______________CAAGU_C__CCG_________AG_UCA__UCUUUGAG\n3'-CGC...GUUUU_____G_AA___AAAUCAAUA__C___AC________AGCUU...AAG-5'\n_____________\|_____________________________________\|\n_____________87____________________________________49\n	206 -- 212	50 -- 56	-25.6976 kcal/mol	9.05881 kcal/mol	4.40785 kcal/mol	183 213@LB@ \| \|@LB@5'-GAU...GACAC G GA A A GA ACCGA...CUU-3'@LB@ GUUCA G GGC UC AGU AGAAACUC@LB@ \|\|\|\|\| \| \|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CAAGU C CCG AG UCA UCUUUGAG@LB@3'-CGC...GUUUU G AA AAAUCAAUA C AC AGCUU...AAG-5'@LB@ \| \|@LB@ 87 49@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -25.6976 kcal/mol@LB@Unfolding Energy - mRNA 9.05881 kcal/mol@LB@Unfolding Energy - sRNA 4.40785 kcal/mol@LB@@LB@Position - mRNA 184 -- 212@LB@Position - sRNA 50 -- 86@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 50 -- 56@LB@
74	0.01362	0.5385	b0946	zapC	-12.02	0.046851	175 -- 197	15 -- 35	FtsZ stabilizer	_____________174_____________________198\n_____________\|_______________________\|\n5'-AUU...GCUGC_______U_____AG________CAGAU...GUU-3'\n______________GGUUUUA_AGGGU__GGGAGAGG\n______________\|::\|\|:\|_\|\|\|\|\|__:::\|\|\|\|\|\n______________CUGAAGU_UCCCA__UUUUCUCC\n3'-CGC...CGUCA_____________A_________ACGGC...AAG-5'\n_____________\|_______________________\|\n_____________36______________________14\n	191 -- 197	15 -- 21	-19.3355 kcal/mol	3.98393 kcal/mol	3.33058 kcal/mol	174 198@LB@ \| \|@LB@5'-AUU...GCUGC U AG CAGAU...GUU-3'@LB@ GGUUUUA AGGGU GGGAGAGG@LB@ \|::\|\|:\| \|\|\|\|\| :::\|\|\|\|\|@LB@ CUGAAGU UCCCA UUUUCUCC@LB@3'-CGC...CGUCA A ACGGC...AAG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -19.3355 kcal/mol@LB@Unfolding Energy - mRNA 3.98393 kcal/mol@LB@Unfolding Energy - sRNA 3.33058 kcal/mol@LB@@LB@Position - mRNA 175 -- 197@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 15 -- 21@LB@
75	0.01364	0.5385	b0107	hofB	-15.68	0.010425	272 -- 289	69 -- 87	T2SE secretion family protein; P-loop ATPase superfamily protein	_____________271_________________290\n_____________\|___________________\|\n5'-CCA...GAGGU_____________GG____CGAUG...CUU-3'\n______________GGUUCAUGUUG_C__UAGU\n______________:\|\|\|\|\|:\|\|\|\|_\|__\|\|\|\|\n______________UCAAGUGCAAC_G__AUCA\n3'-CGC...CGUUU___________C_AA____AUAAG...AAG-5'\n_____________\|___________________\|\n_____________88__________________68\n	276 -- 282	77 -- 83	-18.3354 kcal/mol	2.08484 kcal/mol	0.569189 kcal/mol	271 290@LB@ \| \|@LB@5'-CCA...GAGGU GG CGAUG...CUU-3'@LB@ GGUUCAUGUUG C UAGU@LB@ :\|\|\|\|\|:\|\|\|\| \| \|\|\|\|@LB@ UCAAGUGCAAC G AUCA@LB@3'-CGC...CGUUU C AA AUAAG...AAG-5'@LB@ \| \|@LB@ 88 68@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -18.3354 kcal/mol@LB@Unfolding Energy - mRNA 2.08484 kcal/mol@LB@Unfolding Energy - sRNA 0.569189 kcal/mol@LB@@LB@Position - mRNA 272 -- 289@LB@Position - sRNA 69 -- 87@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 77 -- 83@LB@
76	0.01392	0.5385	b0066	thiQ	-9.74	0.117374	220 -- 232	71 -- 84	thiamine/thiamine pyrophosphate ABC transporter ATPase	_____________219____________233\n_____________\|______________\|\n5'-GCU...UGAUA____C_________CCACC...CAA-3'\n______________UCAC__UGGCUUUA\n______________\|\|\|\|__\|\|\|\|\|\|\|\|\n______________AGUG__ACCGAAAU\n3'-CGC...UUUCA____CA________CAAUA...AAG-5'\n_____________\|______________\|\n_____________85_____________70\n	226 -- 232	71 -- 77	-13.9563 kcal/mol	3.66363 kcal/mol	0.5567 kcal/mol	219 233@LB@ \| \|@LB@5'-GCU...UGAUA C CCACC...CAA-3'@LB@ UCAC UGGCUUUA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGUG ACCGAAAU@LB@3'-CGC...UUUCA CA CAAUA...AAG-5'@LB@ \| \|@LB@ 85 70@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -13.9563 kcal/mol@LB@Unfolding Energy - mRNA 3.66363 kcal/mol@LB@Unfolding Energy - sRNA 0.5567 kcal/mol@LB@@LB@Position - mRNA 220 -- 232@LB@Position - sRNA 71 -- 84@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 71 -- 77@LB@
77	0.01396	0.5385	b3644	yicC	-11.79	0.051421	238 -- 254	15 -- 31	UPF0701 family protein	_____________237_______________255\n_____________\|_________________\|\n5'-UCU...UGAAA________GAAU_____AGCGC...AAA-3'\n______________UCAAGGGU____GGGGG\n______________\|\|\|\|\|\|\|\|____:\|:\|\|\n______________AGUUCCCA____UCUCC\n3'-CGC...ACUGA________AUUU_____ACGGC...AAG-5'\n_____________\|_________________\|\n_____________32________________14\n	239 -- 245	24 -- 30	-20.4957 kcal/mol	5.4171 kcal/mol	3.28624 kcal/mol	237 255@LB@ \| \|@LB@5'-UCU...UGAAA GAAU AGCGC...AAA-3'@LB@ UCAAGGGU GGGGG@LB@ \|\|\|\|\|\|\|\| :\|:\|\|@LB@ AGUUCCCA UCUCC@LB@3'-CGC...ACUGA AUUU ACGGC...AAG-5'@LB@ \| \|@LB@ 32 14@LB@@LB@@LB@Energy -11.79 kcal/mol@LB@Hybridization Energy -20.4957 kcal/mol@LB@Unfolding Energy - mRNA 5.4171 kcal/mol@LB@Unfolding Energy - sRNA 3.28624 kcal/mol@LB@@LB@Position - mRNA 238 -- 254@LB@Position - sRNA 15 -- 31@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 24 -- 30@LB@
78	0.01399	0.5385	b3526	kdgK	-7.99	0.228654	189 -- 197	80 -- 88	2-dehydro-3-deoxygluconokinase	_____________188_______198\n_____________\|_________\|\n5'-CCC...AGAUC_________ACUAU...CUU-3'\n______________AGGUUCACG\n______________\|:\|\|\|\|\|\|\|\n______________UUCAAGUGC\n3'-CGC...GCGUU_________AACCG...AAG-5'\n_____________\|_________\|\n_____________89________79\n	191 -- 197	80 -- 86	-11.7911 kcal/mol	3.29177 kcal/mol	0.504555 kcal/mol	188 198@LB@ \| \|@LB@5'-CCC...AGAUC ACUAU...CUU-3'@LB@ AGGUUCACG@LB@ \|:\|\|\|\|\|\|\|@LB@ UUCAAGUGC@LB@3'-CGC...GCGUU AACCG...AAG-5'@LB@ \| \|@LB@ 89 79@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -11.7911 kcal/mol@LB@Unfolding Energy - mRNA 3.29177 kcal/mol@LB@Unfolding Energy - sRNA 0.504555 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 80 -- 88@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 80 -- 86@LB@
79	0.01412	0.5385	b2830	rppH	-5.99	0.454649	93 -- 100	64 -- 71	RNA pyrophosphohydrolase	_____________92_______101\n_____________\|________\|\n5'-UUC...CUGUG________AAUUG...GGC-3'\n______________AGUUAUUC\n______________\|\|\|\|\|\|\|\|\n______________UCAAUAAG\n3'-CGC...CGAAA________CUCAA...AAG-5'\n_____________\|________\|\n_____________72_______63\n	94 -- 100	64 -- 70	-7.84269 kcal/mol	1.74359 kcal/mol	0.11296 kcal/mol	92 101@LB@ \| \|@LB@5'-UUC...CUGUG AAUUG...GGC-3'@LB@ AGUUAUUC@LB@ \|\|\|\|\|\|\|\|@LB@ UCAAUAAG@LB@3'-CGC...CGAAA CUCAA...AAG-5'@LB@ \| \|@LB@ 72 63@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -7.84269 kcal/mol@LB@Unfolding Energy - mRNA 1.74359 kcal/mol@LB@Unfolding Energy - sRNA 0.11296 kcal/mol@LB@@LB@Position - mRNA 93 -- 100@LB@Position - sRNA 64 -- 71@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 64 -- 70@LB@
80	0.01445	0.5385	b4257	yjgN	-10.51	0.086376	202 -- 215	65 -- 78	DUF898 family inner membrane protein	_____________201____________216\n_____________\|______________\|\n5'-UUA...UUUUA_____CA_______AAUGA...UGU-3'\n______________UGGCU__AGUUAUU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|\n______________ACCGA__UCAAUAA\n3'-CGC...GUGCA_____AA_______GCUCA...AAG-5'\n_____________\|______________\|\n_____________79_____________64\n	209 -- 215	65 -- 71	-13.5706 kcal/mol	2.80573 kcal/mol	0.256929 kcal/mol	201 216@LB@ \| \|@LB@5'-UUA...UUUUA CA AAUGA...UGU-3'@LB@ UGGCU AGUUAUU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|@LB@ ACCGA UCAAUAA@LB@3'-CGC...GUGCA AA GCUCA...AAG-5'@LB@ \| \|@LB@ 79 64@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -13.5706 kcal/mol@LB@Unfolding Energy - mRNA 2.80573 kcal/mol@LB@Unfolding Energy - sRNA 0.256929 kcal/mol@LB@@LB@Position - mRNA 202 -- 215@LB@Position - sRNA 65 -- 78@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 65 -- 71@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)

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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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